ENH: Add initial FastSurfer interface (WIP)

[pcamach2]

Supports #278

Adds FastSurfer detection utility incorporated to smriprep.workflows.anatomical.py to fix failure when providing FastSurfer subjects dir as existing Freesurfer subjects dir. This utility check_fastsurfer employs a fix of touching a labels intensity file expected by Freesurfer, but not currently produced by FastSurfer. FastSurfer outputs from running with the --surfreg flag can then be used to successfully complete the sMRIPrep workflow.

Adds draft of basic interface for FastSurfer to smriprep interfaces, which work on my test datasets when running on the modified Docker or Singularity images (~see f8972dac90f75d7e051723b19e6bb826f1cb696e for changes to Dockerfile~ EDIT: this Dockerfile has been replaced with a version built on Ubuntu 20.04 that passes CircleCI build).

To support the using the FastSurfer interface/wrapper to run FastSurfer as part of sMRIPrep, this PR also adds the following argument to the cli (https://github.com/pcamach2/smriprep/blob/pcamach2-fastsurfer-patch-dev/smriprep/cli/run.py)

    g_surfs_xor.add_argument(
        "--fastsurfer-recon",
        action="store_true",
        dest="run_fastsurfer",
        help="enable FastSurfer surface preprocessing.",
    )

As mentioned in the above issue, I am wondering where best to split workflow behavior (in anatomical.py?) based on the above argument. Would it be better to make separate surfaces.py versions for FastSurfer and FreeSurfer or just different workflows within a unified surfaces.py? Note that if a dataset includes FLAIR or T2w, FreeSurfer will still want to process them automatically even if there is FastSurfer output (this adds on a few hours).

[pep8speaks]

Hello @pcamach2! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2022-09-01 16:21:34 UTC

[effigies]

Thanks! This is helpful for understanding how you've been thinking about it. To lay out my current thinking, the use cases are:

1. I want to/have run FreeSurfer.
2. I want to/have run FastSurfer.
3. I want sMRIPrep to use what it finds, but not attempt to continue.
4. I want sMRIPrep to see what it finds, and attempt to continue with the appropriate tool if results are incomplete.

(1) is implemented with continuation here:

https://github.com/nipreps/smriprep/blob/86c40fa9c2232242b28a0ee2b8ff4805ce9aec07/smriprep/workflows/surfaces.py#L52-L302

For (2), does FastSurfer do this resumption internally? If so, then we can create a copy of that function that replaces most of it with a single call to FastSurfer. If not, then we'll need to do something like with ReconAll to determine the correct command line based on the found contents. And then this can be switched based on your CLI flag, no need for a check_fastsurfer() function.

For (3) I think maybe the better approach than the check_fastsurfer() function would now be one that just looks explicitly for sMRIPrep's expected results (T1.mgz, parcellations/segmentations, surfaces). If those are present, then use a very bare-bones version of init_surface_recon_wf that is just (minus autorecon_resume_wf):

https://github.com/nipreps/smriprep/blob/86c40fa9c2232242b28a0ee2b8ff4805ce9aec07/smriprep/workflows/surfaces.py#L226-L238

We'll also need a FreeSurferSource, e.g.,

https://github.com/nipreps/smriprep/blob/86c40fa9c2232242b28a0ee2b8ff4805ce9aec07/smriprep/workflows/surfaces.py#L605

I don't know that (4) is really worth supporting, because now we have to distinguish between full and partial versions of each type as well as decide what to do if neither is present. Let's let people use flags.

Will respond to your comments in another post.

[effigies]

As mentioned in the above issue, I am wondering where best to split workflow behavior (in anatomical.py?) based on the above argument.

Yes, I think something along the lines of:

if freesurfer:
    recon_wf = init_surface_recon_wf()
elif fastsurfer:
    recon_wf = init_fastsurf_recon_wf()

If we make sure they have the same inputnodes and outputnodes, then very little should need changing.

Would it be better to make separate surfaces.py versions for FastSurfer and FreeSurfer or just different workflows within a unified surfaces.py?

It makes very little difference to me. I would be inclined to keep them in a single place.

Note that if a dataset includes FLAIR or T2w, FreeSurfer will still want to process them automatically even if there is FastSurfer output (this adds on a few hours).

Is pial refinement with FreeSurfer considered a desirable post-FastSurfer step? Assuming not, we should just not duplicate the recon_resume_wf() in the FastSurfer variant.

[pcamach2]

@effigies. Thank you for the feedback and guidance here!

In regards to the use cases not yet supported:

2. I want to/have run FastSurfer
3. I want sMRIPrep to use what it finds, but not attempt to continue.
4. I want sMRIPrep to see what it finds, and attempt to continue with the appropriate tool if results are incomplete.

I agree that trying to support (4) is not worth the granularity in file checks that would be necessary to distinguish between the two. Related to (2) also, FastSurfer specifies that the directory for a subject within sd (equivalent to fs subjects_dir) should be empty prior to running - so it seems that resumption is not internally supported, but I am hesitant to resume with a faulty/incomplete directory. Although not implemented here, the associated QATools would likely give very little useful metrics with a messy recon log (as seen in restarted Freesurfer runs https://github.com/Deep-MI/qatools-python#known-issues).

For (2), does FastSurfer do this resumption internally? If so, then we can create a copy of that function that replaces most of it with a single call to FastSurfer. If not, then we'll need to do something like with ReconAll to determine the correct command line based on the found contents. And then this can be switched based on your CLI flag, no need for a check_fastsurfer() function.

The only supported resume here seems to be running recon-surf with only the segmentation from FastSurfer CNN present, which can be achieved with the --surf_only argument to the FastSurfer commandline tool. ~If it is worthwhile, we could check for the FastSurfer CNN outputs and - if only those outputs are present - pass the --surf_only argument in the FastSurfer command.~ EDIT: Due to the relatively low run time for segmentation with FastSurfer CNN, I doubt that most folks will have a real need for the above striked function.

For (3) I think maybe the better approach than the check_fastsurfer() function would now be one that just looks explicitly for sMRIPrep's expected results (T1.mgz, parcellations/segmentations, surfaces). If those are present, then use a very bare-bones version of init_surface_recon_wf that is just (minus autorecon_resume_wf):

https://github.com/nipreps/smriprep/blob/86c40fa9c2232242b28a0ee2b8ff4805ce9aec07/smriprep/workflows/surfaces.py#L226-L238

We'll also need a FreeSurferSource, e.g.,

https://github.com/nipreps/smriprep/blob/86c40fa9c2232242b28a0ee2b8ff4805ce9aec07/smriprep/workflows/surfaces.py#L605

That sounds good to me!

As mentioned in the above issue, I am wondering where best to split workflow behavior (in anatomical.py?) based on the above argument.

Yes, I think something along the lines of:

if freesurfer:
    recon_wf = init_surface_recon_wf()
elif fastsurfer:
    recon_wf = init_fastsurf_recon_wf()

If we make sure they have the same inputnodes and outputnodes, then very little should need changing.

Would it be better to make separate surfaces.py versions for FastSurfer and FreeSurfer or just different workflows within a unified surfaces.py?

It makes very little difference to me. I would be inclined to keep them in a single place.

Note that if a dataset includes FLAIR or T2w, FreeSurfer will still want to process them automatically even if there is FastSurfer output (this adds on a few hours).

Is pial refinement with FreeSurfer considered a desirable post-FastSurfer step? Assuming not, we should just not duplicate the recon_resume_wf() in the FastSurfer variant.

I am not sure that pial refinement with FreeSurfer is actually a good idea, especially with FreeSurfer 6.X (this is discussed in an issue here: https://github.com/Deep-MI/FastSurfer/issues/89#issuecomment-999421061), so I agree that not duplicating the recon_resume_wf() in a FastSurfer is a better choice for now. This might be something to revisit as FreeSurfer 7.X is updated.

I am open to other ideas, but I lean towards the following changes to get things going here (in descending order of importance):

• [x] create a function to detect the inputs sMRIPrep expects from surface recon
• [x] creating the init_fastsurf_recon_wf in surfaces.py as you suggested
• [x] replacing the check_fastsurfer function use with the superseding CLI fastsurfer argument to make sure users are purposely choosing FastSurfer over FreeSurfer
• [ ] updating the documentation to include FastSurfer in the description

Please let me know what you think and I can get started on these in this draft PR or a different PR if appropriate. Thanks again!

[pcamach2]

@effigies, I've tried a number of different fixes for this, but I have not been able to resolve the following ci/circleci: build_docs error:

Warning, treated as error:
/tmp/gh-pages/smriprep/interfaces/fastsurfer.py:docstring of smriprep.interfaces.fastsurfer.FastSCommand:37:Definition list ends without a blank line; unexpected unindent.
make: *** [Makefile:61: html] Error 2
make: Leaving directory '/tmp/gh-pages/docs'

Exited with code exit status 2

CircleCI received exit code 2

The docstring for smriprep/interfaces/fastsurfer.py that is mentioned in the warning is:

class FastSCommand(CommandLine):
    """
    Wraps FastSurfer command for segmentation and surface processing

    """

    input_spec = FastSInputSpec
    output_spec = FastSurfSourceOutputSpec
    _cmd = '/fastsurfer/run_fastsurfer.sh'

    def _list_outputs(self):
        outputs = self.output_spec().get()
        return outputs

[effigies]

Thanks. I'll try to have a look this weekend.

[pcamach2]

As an update on the FastSurfer wrapper, the overall workflow is failing to complete:

singularity run --nv -B ./bids:/data,./bids/derivatives:/out,/redacted-data/singularity_images/fslicense/license.txt:/opt/freesurfer/license.txt /redacted-data/singularity_images/smriprep_test/smriprep/smriprep_fastsurfer.sif /data/ /out/ --fs-subjects-dir /out/fastsurfer --fs-license-file /opt/freesurfer/license.txt --fastsurfer participant --participant-label sub-SUB307
220504-15:33:47,123 nipype.workflow Level 25:
	 
    Running sMRIPrep version :
      * BIDS dataset path: /data.
      * Participant list: ['SUB307'].
      * Run identifier: 20220504-153230_f75c3f2c-b6fd-4287-8879-0d4daf0bb6d9.

    Spatial References: <none>.
    
220504-15:33:47,593 nipype.utils WARNING:
	 A newer version (1.7.1) of nipy/nipype is available. You are using 1.6.1
220504-15:33:57,214 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.6.1
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset.The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.3.3 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 6.0.5.1:57b01774, RRID:SCR_002823,
@fsl_fast].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


220504-15:34:04,172 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.brain_extraction_wf.full_wm" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/brain_extraction_wf/full_wm".
220504-15:34:04,182 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_norm_wf/outputnode".
220504-15:34:04,214 nipype.workflow INFO:
	 [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface")
220504-15:34:04,220 nipype.workflow INFO:
	 [Node] Running "full_wm" ("nipype.interfaces.utility.wrappers.Function")
220504-15:34:04,359 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_norm_wf.outputnode".
220504-15:34:04,414 nipype.workflow WARNING:
	 Storing result file without outputs
220504-15:34:04,419 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_fwd" (/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_fwd)
220504-15:34:04,430 nipype.workflow ERROR:
	 Node lta2itk_fwd failed to run on host redacted.
220504-15:34:04,433 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB307/log/20220504-153230_f75c3f2c-b6fd-4287-8879-0d4daf0bb6d9/crash-20220504-153404-pcamach2-lta2itk_fwd-f32536ea-6629-4823-88c7-381c5fb451ec.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/nitransforms.py", line 82, in _run_interface
    concatenate_xfms(
  File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/nitransforms.py", line 101, in concatenate_xfms
    [load_affine(f, fmt=XFM_FMT[Path(f).suffix]) for f in in_files]
TypeError: '_Undefined' object is not iterable

220504-15:34:04,551 nipype.workflow WARNING:
	 Storing result file without outputs
220504-15:34:04,555 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_inv" (/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_inv)
220504-15:34:04,558 nipype.workflow ERROR:
	 Node lta2itk_inv failed to run on host redacted.
220504-15:34:04,559 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB307/log/20220504-153230_f75c3f2c-b6fd-4287-8879-0d4daf0bb6d9/crash-20220504-153404-pcamach2-lta2itk_inv-b57cea13-d966-43aa-b073-23e0ef315f00.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/nitransforms.py", line 82, in _run_interface
    concatenate_xfms(
  File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/nitransforms.py", line 101, in concatenate_xfms
    [load_affine(f, fmt=XFM_FMT[Path(f).suffix]) for f in in_files]
TypeError: '_Undefined' object is not iterable

220504-15:34:04,577 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl".
220504-15:34:04,586 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl".
220504-15:34:04,648 nipype.workflow INFO:
	 [Node] Running "res_tmpl" ("niworkflows.interfaces.nibabel.RegridToZooms")
220504-15:34:04,651 nipype.workflow INFO:
	 [Node] Running "lap_tmpl" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1
220504-15:34:04,758 nipype.workflow ERROR:
	 Node name_surfs failed to run on host redacted.
220504-15:34:04,759 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB307/log/20220504-153230_f75c3f2c-b6fd-4287-8879-0d4daf0bb6d9/crash-20220504-153404-pcamach2-name_surfs-9e8ffb52-d2e3-407b-8fba-aef1cb9abee2.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 292, in _send_procs_to_workers
    num_subnodes = self.procs[jobid].num_subnodes()
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 1309, in num_subnodes
    self._check_iterfield()
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 1332, in _check_iterfield
    raise ValueError(
ValueError: Input in_file was not set but it is listed in iterfields.


When creating this crashfile, the results file corresponding
to the node could not be found.
220504-15:34:05,419 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.brain_extraction_wf.full_wm".
220504-15:34:06,746 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl".
220504-15:34:08,636 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.bidssrc" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/bidssrc".
220504-15:34:08,657 nipype.workflow INFO:
	 [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
220504-15:34:08,704 nipype.interface INFO:
	 No "roi" images found for sub-<undefined>
220504-15:34:08,726 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB307_wf.bidssrc".
220504-15:34:09,959 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions".
220504-15:34:10,120 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_reports_wf.recon_report" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_reports_wf/recon_report".
220504-15:34:10,137 nipype.workflow INFO:
	 [Node] Running "recon_report" ("smriprep.interfaces.reports.FastSurfSurfaceReport")
220504-15:34:10,138 nipype.workflow WARNING:
	 Storing result file without outputs
220504-15:34:10,141 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_reports_wf.recon_report" (/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_reports_wf/recon_report)
220504-15:34:11,154 nipype.workflow ERROR:
	 Node recon_report failed to run on host redacted.
220504-15:34:11,155 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB307/log/20220504-153230_f75c3f2c-b6fd-4287-8879-0d4daf0bb6d9/crash-20220504-153411-pcamach2-recon_report-32150616-131d-4bf6-902b-fd10fb89c99a.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 383, in run
    self._check_mandatory_inputs()
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 264, in _check_mandatory_inputs
    raise ValueError(msg)
ValueError: FastSurfSurfaceReport requires a value for input 'sd'. For a list of required inputs, see FastSurfSurfaceReport.help()

220504-15:34:11,520 nipype.utils WARNING:
	 A newer version (1.7.1) of nipy/nipype is available. You are using 1.6.1
220504-15:34:15,562 nipype.workflow INFO:
	 [Node] Running "t1w_ref_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
220504-15:34:15,687 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions".
220504-15:34:17,437 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources".
220504-15:34:17,460 nipype.workflow WARNING:
	 Storing result file without outputs
220504-15:34:17,465 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1w_fsaseg" (/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1w_fsaseg)
220504-15:34:17,469 nipype.workflow ERROR:
	 Node ds_t1w_fsaseg failed to run on host redacted.
220504-15:34:17,470 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB307/log/20220504-153230_f75c3f2c-b6fd-4287-8879-0d4daf0bb6d9/crash-20220504-153417-pcamach2-ds_t1w_fsaseg-4272f2a5-cce2-428a-bab1-d5e520c6310f.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 383, in run
    self._check_mandatory_inputs()
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 264, in _check_mandatory_inputs
    raise ValueError(msg)
ValueError: DerivativesDataSink requires a value for input 'in_file'. For a list of required inputs, see DerivativesDataSink.help()

220504-15:34:17,587 nipype.workflow WARNING:
	 Storing result file without outputs
220504-15:34:17,591 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB307_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1w_fsparc" (/redacted-ignite/SUB/work/smriprep_wf/single_subject_SUB307_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1w_fsparc)
220504-15:34:17,605 nipype.workflow ERROR:
	 Node ds_t1w_fsparc failed to run on host redacted.
220504-15:34:17,606 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB307/log/20220504-153230_f75c3f2c-b6fd-4287-8879-0d4daf0bb6d9/crash-20220504-153417-pcamach2-ds_t1w_fsparc-f96108f8-a01e-432a-922b-a8a726b18901.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 383, in run
    self._check_mandatory_inputs()
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 264, in _check_mandatory_inputs
    raise ValueError(msg)
ValueError: DerivativesDataSink requires a value for input 'in_file'. For a list of required inputs, see DerivativesDataSink.help()

The following items need to be addressed

• [ ] build_docs fails for FastSCommand
• [x] switch Docker build from FastSurfer dev branch to stable branch or upgrade to FreeSurfer 7.2
• [ ] workflow errors in DerivativesDataSink missing 'in_file'
• [ ] error in FastSurfSurfaceReport not finding sd
• [ ] CircleCI test of FastSurfer workflow?

[effigies]

@pcamach2 This is just to check in. Sorry, I'm very unlikely to get to this before May 31, at this point. I apologize for the delays. If it's any consolation, I'm trying to get FreeSurfer 7.2 working in fMRIPrep, so hopefully there's some synergy here.

[pcamach2]

@effigies, no worries! I have been writing up my preliminary exam so I had to put this on pause for a bit. Including FreeSurfer 7.2 sounds great! That will definitely facilitate FastSurfer VINN when the time comes

[pcamach2]

@effigies, I've made some progress and my local singularity image - based on this Dockerfile - runs most of the FastSurfer rountine, but there are some more immediate bugs to work out in the overall nipype workflow that I set up. I'm not sure if these are related to the recent updates to Freesurfer or sMRIPrep or just my own errors, so any guidance/advice would be greatly appreciated!

Here is the current output from a test that is currently running:

-bash-4.2$ singularity run --nv -B ./bids:/data,./bids/derivatives:/out,./bids/derivatives/fastsurfer:/out/freesurfer,/redacted/singularity_images/fslicense/license.txt:/opt/freesurfer/license.txt /redacted/singularity_images/smriprep_test/fresh/smriprep/smriprep_fastsurfer_stable.sif /data/ /out/ --participant-label sub-SUB497 --output-spaces MNI152NLin2009cAsym --fastsurfer --fs-license-file /opt/freesurfer/license.txt participant
220706-13:51:22,324 nipype.workflow Level 25:
	 
    Running sMRIPrep version :
      * BIDS dataset path: /data.
      * Participant list: ['SUB497'].
      * Run identifier: 20220706-135052_dba74e89-7d41-43be-8270-ba38b3d4294e.

    Spatial References: MNI152NLin2009cAsym:res-native
    
220706-13:51:24,839 nipype.workflow WARNING:
	 High-resolution True specified, not currently supported, ignoring.
220706-13:51:27,924 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.8.2
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset.The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.3.3 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 6.0.5.1:57b01774, RRID:SCR_002823,
@fsl_fast].
Brain surfaces were reconstructed using `recon-surf` [FastSurfer 1.1.0,
@fastsurfer], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FastSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Volume-based spatial normalization to one standard space (MNI152NLin2009cAsym) was performed through
nonlinear registration with `antsRegistration` (ANTs 2.3.3),
using brain-extracted versions of both T1w reference and the T1w template.
The following template was selected for spatial normalization:
*ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


220706-13:51:31,914 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.full_wm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/full_wm".
220706-13:51:31,932 nipype.workflow INFO:
	 [Node] Executing "full_wm" <nipype.interfaces.utility.wrappers.Function>
220706-13:51:32,115 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl".
220706-13:51:32,145 nipype.workflow INFO:
	 [Node] Executing "lap_tmpl" <nipype.interfaces.ants.utils.ImageMath>
220706-13:51:32,165 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl".
220706-13:51:32,258 nipype.workflow INFO:
	 [Node] Executing "res_tmpl" <niworkflows.interfaces.nibabel.RegridToZooms>
220706-13:51:32,978 nipype.workflow INFO:
	 [Node] Finished "full_wm", elapsed time 1.018796s.
220706-13:51:34,307 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.bidssrc" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/bidssrc".
220706-13:51:34,349 nipype.workflow INFO:
	 [Node] Finished "res_tmpl", elapsed time 2.062386s.
220706-13:51:34,364 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.segs_to_native_aseg.fs_datasource" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/segs_to_native_aseg/fs_datasource".
220706-13:51:34,431 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <smriprep.interfaces.fastsurfer.FastSurferSource>
220706-13:51:34,465 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.000564s.
220706-13:51:34,465 nipype.workflow WARNING:
	 Storing result file without outputs
220706-13:51:34,469 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.segs_to_native_aseg.fs_datasource" (/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/segs_to_native_aseg/fs_datasource)
220706-13:51:34,493 nipype.workflow INFO:
	 [Node] Executing "bidssrc" <niworkflows.interfaces.bids.BIDSDataGrabber>
220706-13:51:34,541 nipype.interface INFO:
	 No "t2w" images found for sub-<undefined>
220706-13:51:34,541 nipype.interface INFO:
	 No "flair" images found for sub-<undefined>
220706-13:51:34,541 nipype.interface INFO:
	 No "roi" images found for sub-<undefined>
220706-13:51:34,542 nipype.workflow INFO:
	 [Node] Finished "bidssrc", elapsed time 0.001119s.
220706-13:51:34,558 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/segs_to_native_aparc_aseg/fs_datasource".
220706-13:51:34,649 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <smriprep.interfaces.fastsurfer.FastSurferSource>
220706-13:51:34,679 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.000733s.
220706-13:51:34,679 nipype.workflow WARNING:
	 Storing result file without outputs
220706-13:51:34,683 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.segs_to_native_aparc_aseg.fs_datasource" (/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/segs_to_native_aparc_aseg/fs_datasource)
220706-13:51:35,220 nipype.workflow ERROR:
	 Node fs_datasource failed to run on host host.host.
220706-13:51:35,224 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB497/log/20220706-135052_dba74e89-7d41-43be-8270-ba38b3d4294e/crash-20220706-135135-pcamach2-fs_datasource-2f4e54bd-d40f-49d5-a821-4a4e806a9d7d.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node fs_datasource.

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 430, in aggregate_outputs
    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
  File "/opt/conda/lib/python3.8/site-packages/smriprep/interfaces/fastsurfer.py", line 650, in _list_outputs
    subject_path = os.path.join(subjects_dir, subject_id)
  File "/opt/conda/lib/python3.8/posixpath.py", line 76, in join
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not _Undefined


220706-13:51:35,239 nipype.workflow ERROR:
	 Node fs_datasource failed to run on host host.host.
220706-13:51:35,240 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB497/log/20220706-135052_dba74e89-7d41-43be-8270-ba38b3d4294e/crash-20220706-135135-pcamach2-fs_datasource-5f3c48e8-4fd1-491f-99a8-111fe0856b0e.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node fs_datasource.

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 430, in aggregate_outputs
    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
  File "/opt/conda/lib/python3.8/site-packages/smriprep/interfaces/fastsurfer.py", line 650, in _list_outputs
    subject_path = os.path.join(subjects_dir, subject_id)
  File "/opt/conda/lib/python3.8/posixpath.py", line 76, in join
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not _Undefined


220706-13:51:35,755 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions".
220706-13:51:37,605 nipype.workflow INFO:
	 [Node] Executing "t1w_ref_dimensions" <niworkflows.interfaces.images.TemplateDimensions>
220706-13:51:37,744 nipype.workflow INFO:
	 [Node] Finished "t1w_ref_dimensions", elapsed time 0.091788s.
220706-13:51:39,593 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources".
220706-13:51:39,878 nipype.workflow INFO:
	 [Node] Setting-up "_t1w_conform0" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/anat_template_wf/t1w_conform/mapflow/_t1w_conform0".
220706-13:51:39,917 nipype.workflow INFO:
	 [Node] Executing "_t1w_conform0" <niworkflows.interfaces.images.Conform>
220706-13:51:40,85 nipype.workflow INFO:
	 [Node] Executing "raw_sources" <nipype.interfaces.utility.wrappers.Function>
220706-13:51:40,97 nipype.workflow INFO:
	 [Node] Finished "_t1w_conform0", elapsed time 0.136989s.
220706-13:51:40,104 nipype.workflow INFO:
	 [Node] Finished "raw_sources", elapsed time 0.000447s.
220706-13:51:40,430 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.gifti_surface_wf.get_surfaces" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/gifti_surface_wf/get_surfaces".
220706-13:51:40,478 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <smriprep.interfaces.fastsurfer.FastSurferSource>
220706-13:51:40,558 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.035458s.
220706-13:51:40,559 nipype.workflow WARNING:
	 Storing result file without outputs
220706-13:51:40,562 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.gifti_surface_wf.get_surfaces" (/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/gifti_surface_wf/get_surfaces)
220706-13:51:40,654 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.anat_reports_wf.recon_report" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/anat_reports_wf/recon_report".
220706-13:51:40,719 nipype.workflow INFO:
	 [Node] Executing "recon_report" <smriprep.interfaces.reports.FastSurfSurfaceReport>
220706-13:51:41,229 nipype.workflow ERROR:
	 Node get_surfaces failed to run on host host.host.
220706-13:51:41,231 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB497/log/20220706-135052_dba74e89-7d41-43be-8270-ba38b3d4294e/crash-20220706-135141-pcamach2-get_surfaces-b6c566ce-0b12-42b1-abd6-0a28835b4d76.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node get_surfaces.

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 430, in aggregate_outputs
    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
  File "/opt/conda/lib/python3.8/site-packages/smriprep/interfaces/fastsurfer.py", line 654, in _list_outputs
    val = self._get_files(
  File "/opt/conda/lib/python3.8/site-packages/smriprep/interfaces/fastsurfer.py", line 642, in _get_files
    globfmt = os.path.join(path, dirval, "".join((globprefix, "{}", globsuffix)))
  File "/opt/conda/lib/python3.8/posixpath.py", line 90, in join
    genericpath._check_arg_types('join', a, *p)
  File "/opt/conda/lib/python3.8/genericpath.py", line 152, in _check_arg_types
    raise TypeError(f'{funcname}() argument must be str, bytes, or '
TypeError: join() argument must be str, bytes, or os.PathLike object, not 'NoneType'


220706-13:51:41,313 nipype.workflow INFO:
	 [Node] Finished "lap_tmpl", elapsed time 9.022328s.
220706-13:51:41,336 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.anat_template_wf.get1st" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/anat_template_wf/get1st".
220706-13:51:41,674 nipype.workflow INFO:
	 [Node] Executing "get1st" <nipype.interfaces.utility.base.Select>
220706-13:51:41,702 nipype.workflow INFO:
	 [Node] Finished "get1st", elapsed time 0.00032s.
/opt/conda/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
  warn("Fetchers from the nilearn.datasets module will be "
220706-13:51:43,313 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl".
220706-13:51:43,595 nipype.workflow INFO:
	 [Node] Executing "mrg_tmpl" <nipype.interfaces.utility.base.Merge>
220706-13:51:43,622 nipype.workflow INFO:
	 [Node] Finished "mrg_tmpl", elapsed time 0.00024s.
220706-13:51:45,586 nipype.workflow INFO:
	 [Node] Setting-up "_truncate_images0" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0".
220706-13:51:45,633 nipype.workflow INFO:
	 [Node] Executing "_truncate_images0" <nipype.interfaces.ants.utils.ImageMath>
220706-13:51:47,674 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.fastsurf_recon" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/fastsurf_recon".
220706-13:51:47,693 nipype.workflow INFO:
	 [Node] Executing "fastsurf_recon" <smriprep.interfaces.fastsurfer.FastSCommand>
220706-13:51:59,585 nipype.workflow INFO:
	 [Node] Finished "_truncate_images0", elapsed time 13.817558s.
220706-13:52:00,113 nipype.workflow INFO:
	 [Node] Finished "recon_report", elapsed time 19.35304s.
220706-13:52:01,831 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n40" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40".
220706-13:52:01,894 nipype.workflow INFO:
	 [Node] Executing "_inu_n40" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
220706-13:53:12,747 nipype.workflow INFO:
	 [Node] Finished "_inu_n40", elapsed time 70.716843s.
220706-13:53:13,693 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/lap_target".
220706-13:53:13,739 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/res_target".
220706-13:53:14,208 nipype.workflow INFO:
	 [Node] Executing "lap_target" <nipype.interfaces.ants.utils.ImageMath>
220706-13:53:15,78 nipype.workflow INFO:
	 [Node] Executing "res_target" <niworkflows.interfaces.nibabel.RegridToZooms>
220706-13:53:17,121 nipype.workflow INFO:
	 [Node] Finished "res_target", elapsed time 1.994699s.
220706-13:53:17,687 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/init_aff".
220706-13:53:17,806 nipype.workflow INFO:
	 [Node] Executing "init_aff" <nipype.interfaces.ants.utils.AI>
220706-13:53:30,496 nipype.workflow INFO:
	 [Node] Finished "lap_target", elapsed time 16.127158s.
220706-13:53:31,490 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/mrg_target".
220706-13:53:31,731 nipype.workflow INFO:
	 [Node] Executing "mrg_target" <nipype.interfaces.utility.base.Merge>
220706-13:53:31,750 nipype.workflow INFO:
	 [Node] Finished "mrg_target", elapsed time 0.000179s.
220706-13:53:36,930 nipype.workflow INFO:
	 [Node] Finished "init_aff", elapsed time 18.994742s.
220706-13:53:37,773 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/norm".
220706-13:53:37,828 nipype.workflow INFO:
	 [Node] Executing "norm" <niworkflows.interfaces.fixes.FixHeaderRegistration>
220706-14:01:15,563 nipype.workflow INFO:
	 [Node] Finished "norm", elapsed time 457.601891s.
220706-14:01:16,776 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask".
220706-14:01:16,823 nipype.workflow INFO:
	 [Node] Executing "map_brainmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
220706-14:01:16,831 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.map_wmmask" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/map_wmmask".
220706-14:01:16,861 nipype.workflow INFO:
	 [Node] Executing "map_wmmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
220706-14:01:41,633 nipype.workflow INFO:
	 [Node] Finished "map_brainmask", elapsed time 24.690712s.
220706-14:01:42,732 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask".
220706-14:01:42,985 nipype.workflow INFO:
	 [Node] Executing "thr_brainmask" <nipype.interfaces.ants.utils.ThresholdImage>
220706-14:01:42,987 nipype.workflow INFO:
	 [Node] Finished "map_wmmask", elapsed time 26.010992s.
220706-14:01:44,806 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
220706-14:01:44,846 nipype.workflow INFO:
	 [Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
220706-14:01:44,849 nipype.workflow INFO:
	 [Node] Finished "thr_brainmask", elapsed time 1.7172070000000001s.
220706-14:01:46,740 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
220706-14:01:46,741 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
220706-14:01:46,759 nipype.workflow INFO:
	 [Node] Executing "03_pad_mask" <nipype.interfaces.ants.utils.ImageMath>
220706-14:01:46,827 nipype.workflow INFO:
	 [Node] Executing "dil_brainmask" <nipype.interfaces.ants.utils.ImageMath>
220706-14:01:47,822 nipype.workflow INFO:
	 [Node] Finished "03_pad_mask", elapsed time 0.97178s.
220706-14:01:48,995 nipype.workflow INFO:
	 [Node] Finished "dil_brainmask", elapsed time 2.013898s.
220706-14:01:50,752 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/get_brainmask".
220706-14:01:50,778 nipype.workflow INFO:
	 [Node] Executing "get_brainmask" <nipype.interfaces.ants.utils.ImageMath>
220706-14:01:52,738 nipype.workflow INFO:
	 [Node] Finished "get_brainmask", elapsed time 1.864234s.
220706-14:02:11,661 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0", elapsed time 26.662833s.
220706-14:02:12,801 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos".
220706-14:02:12,820 nipype.workflow INFO:
	 [Node] Executing "01_atropos" <nipype.interfaces.ants.segmentation.Atropos>
220706-14:02:13,473 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
220706-14:02:13,563 nipype.workflow INFO:
	 [Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
220706-14:02:14,791 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0", elapsed time 1.180322s.
220706-14:03:14,161 nipype.workflow INFO:
	 [Node] Finished "01_atropos", elapsed time 61.215037s.
220706-14:03:14,970 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
220706-14:03:15,52 nipype.workflow INFO:
	 [Node] Executing "02_pad_segm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:16,377 nipype.workflow INFO:
	 [Node] Finished "02_pad_segm", elapsed time 1.167s.
220706-14:03:16,721 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
220706-14:03:16,996 nipype.workflow INFO:
	 [Node] Executing "04_sel_labels" <nipype.interfaces.utility.wrappers.Function>
220706-14:03:17,779 nipype.workflow INFO:
	 [Node] Finished "04_sel_labels", elapsed time 0.750437s.
220706-14:03:21,183 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm".
220706-14:03:21,190 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf".
220706-14:03:21,193 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm".
220706-14:03:21,193 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
220706-14:03:21,218 nipype.workflow INFO:
	 [Node] Executing "05_get_wm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:21,221 nipype.workflow INFO:
	 [Node] Executing "27_depad_csf" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:21,221 nipype.workflow INFO:
	 [Node] Executing "06_get_gm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:21,260 nipype.workflow INFO:
	 [Node] Executing "10_me_csf" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:22,151 nipype.workflow INFO:
	 [Node] Finished "27_depad_csf", elapsed time 0.816945s.
220706-14:03:23,541 nipype.workflow INFO:
	 [Node] Finished "05_get_wm", elapsed time 2.217268s.
220706-14:03:24,396 nipype.workflow INFO:
	 [Node] Finished "06_get_gm", elapsed time 3.066459s.
220706-14:03:25,12 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
220706-14:03:25,248 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
220706-14:03:25,248 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
220706-14:03:25,308 nipype.workflow INFO:
	 [Node] Executing "09_relabel_wm" <nipype.interfaces.ants.utils.MultiplyImages>
220706-14:03:25,318 nipype.workflow INFO:
	 [Node] Executing "07_fill_gm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:25,389 nipype.workflow INFO:
	 [Node] Executing "apply_wm_prior" <nipype.interfaces.utility.wrappers.Function>
220706-14:03:26,744 nipype.workflow INFO:
	 [Node] Finished "apply_wm_prior", elapsed time 1.307109s.
220706-14:03:26,931 nipype.workflow INFO:
	 [Node] Finished "10_me_csf", elapsed time 5.570292s.
220706-14:03:26,970 nipype.workflow INFO:
	 [Node] Finished "09_relabel_wm", elapsed time 1.520367s.
220706-14:03:27,287 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/inu_n4_final/mapflow/_inu_n4_final0".
220706-14:03:27,370 nipype.workflow INFO:
	 [Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
220706-14:03:29,206 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
220706-14:03:29,307 nipype.workflow INFO:
	 [Node] Executing "26_depad_wm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:30,570 nipype.workflow INFO:
	 [Node] Finished "26_depad_wm", elapsed time 1.108485s.
220706-14:03:40,787 nipype.workflow INFO:
	 [Node] Finished "07_fill_gm", elapsed time 15.346621s.
220706-14:03:41,273 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
220706-14:03:41,321 nipype.workflow INFO:
	 [Node] Executing "08_mult_gm" <nipype.interfaces.ants.utils.MultiplyImages>
220706-14:03:43,229 nipype.workflow INFO:
	 [Node] Finished "08_mult_gm", elapsed time 1.784238s.
220706-14:03:45,283 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm".
220706-14:03:45,327 nipype.workflow INFO:
	 [Node] Executing "11_add_gm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:51,632 nipype.workflow INFO:
	 [Node] Finished "11_add_gm", elapsed time 6.149866s.
220706-14:03:53,299 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
220706-14:03:53,940 nipype.workflow INFO:
	 [Node] Executing "12_relabel_gm" <nipype.interfaces.ants.utils.MultiplyImages>
220706-14:03:55,862 nipype.workflow INFO:
	 [Node] Finished "12_relabel_gm", elapsed time 1.7711540000000001s.
220706-14:03:56,369 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0", elapsed time 28.850341s.
220706-14:03:57,314 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
220706-14:03:57,314 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
220706-14:03:57,332 nipype.workflow INFO:
	 [Node] Executing "13_add_gm_wm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:57,380 nipype.workflow INFO:
	 [Node] Executing "25_depad_gm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:03:58,718 nipype.workflow INFO:
	 [Node] Finished "25_depad_gm", elapsed time 1.192777s.
220706-14:03:59,90 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms".
220706-14:03:59,350 nipype.workflow INFO:
	 [Node] Executing "merge_tpms" <nipype.interfaces.utility.base.Merge>
220706-14:03:59,376 nipype.workflow INFO:
	 [Node] Finished "merge_tpms", elapsed time 0.000221s.
220706-14:04:03,877 nipype.workflow INFO:
	 [Node] Finished "13_add_gm_wm", elapsed time 6.428159s.
220706-14:04:05,101 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
220706-14:04:05,330 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
220706-14:04:05,343 nipype.workflow INFO:
	 [Node] Executing "14_sel_labels2" <nipype.interfaces.utility.wrappers.Function>
220706-14:04:05,345 nipype.workflow INFO:
	 [Node] Executing "24_depad_segm" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:06,5 nipype.workflow INFO:
	 [Node] Finished "14_sel_labels2", elapsed time 0.641189s.
220706-14:04:06,584 nipype.workflow INFO:
	 [Node] Finished "24_depad_segm", elapsed time 1.108491s.
220706-14:04:07,333 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7".
220706-14:04:07,351 nipype.workflow INFO:
	 [Node] Executing "15_add_7" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:12,705 nipype.workflow INFO:
	 [Node] Finished "15_add_7", elapsed time 5.224585s.
220706-14:04:13,351 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7".
220706-14:04:13,429 nipype.workflow INFO:
	 [Node] Executing "16_me_7" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:17,422 nipype.workflow INFO:
	 [Node] Finished "16_me_7", elapsed time 3.829697s.
220706-14:04:19,346 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7".
220706-14:04:19,383 nipype.workflow INFO:
	 [Node] Executing "17_comp_7" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:22,30 nipype.workflow INFO:
	 [Node] Finished "17_comp_7", elapsed time 2.492048s.
220706-14:04:23,284 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7".
220706-14:04:23,300 nipype.workflow INFO:
	 [Node] Executing "18_md_7" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:25,936 nipype.workflow INFO:
	 [Node] Finished "18_md_7", elapsed time 2.529499s.
220706-14:04:27,378 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7".
220706-14:04:27,417 nipype.workflow INFO:
	 [Node] Executing "19_fill_7" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:41,916 nipype.workflow INFO:
	 [Node] Finished "19_fill_7", elapsed time 14.364999s.
220706-14:04:43,428 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
220706-14:04:43,592 nipype.workflow INFO:
	 [Node] Executing "20_add_7_2" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:49,347 nipype.workflow INFO:
	 [Node] Finished "20_add_7_2", elapsed time 5.614713s.
220706-14:04:51,458 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
220706-14:04:51,479 nipype.workflow INFO:
	 [Node] Executing "21_md_7_2" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:54,4 nipype.workflow INFO:
	 [Node] Finished "21_md_7_2", elapsed time 2.369327s.
220706-14:04:55,499 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
220706-14:04:55,517 nipype.workflow INFO:
	 [Node] Executing "22_me_7_2" <nipype.interfaces.ants.utils.ImageMath>
220706-14:04:59,523 nipype.workflow INFO:
	 [Node] Finished "22_me_7_2", elapsed time 3.864462s.
220706-14:05:01,469 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
220706-14:05:01,519 nipype.workflow INFO:
	 [Node] Executing "23_depad_mask" <nipype.interfaces.ants.utils.ImageMath>
220706-14:05:02,711 nipype.workflow INFO:
	 [Node] Finished "23_depad_mask", elapsed time 1.050771s.
220706-14:05:03,250 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/msk_conform".
220706-14:05:03,595 nipype.workflow INFO:
	 [Node] Executing "msk_conform" <nipype.interfaces.utility.wrappers.Function>
220706-14:05:04,113 nipype.workflow INFO:
	 [Node] Finished "msk_conform", elapsed time 0.499007s.
220706-14:05:16,820 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_mask/mapflow/_apply_mask0".
220706-14:05:16,861 nipype.workflow INFO:
	 [Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
220706-14:05:18,446 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0", elapsed time 1.539491s.
220706-14:05:19,846 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.anat_derivatives_wf.gen_ref" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin2009cAsym.resnative/gen_ref".
220706-14:05:19,857 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.anat_norm_wf.trunc_mov" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/trunc_mov".
220706-14:05:19,996 nipype.workflow INFO:
	 [Node] Executing "trunc_mov" <nipype.interfaces.ants.utils.ImageMath>
220706-14:05:21,715 nipype.workflow INFO:
	 [Node] Executing "gen_ref" <niworkflows.interfaces.nibabel.GenerateSamplingReference>
220706-14:05:21,810 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB497_wf.anat_preproc_wf.fastsurf_recon_wf.skull_strip_extern" in "/redacted/SUB/work/smriprep_wf/single_subject_SUB497_wf/anat_preproc_wf/fastsurf_recon_wf/skull_strip_extern".
220706-14:05:22,486 nipype.workflow INFO:
	 [Node] Executing "skull_strip_extern" <niworkflows.interfaces.freesurfer.FSInjectBrainExtracted>
220706-14:05:24,569 nipype.workflow INFO:
	 [Node] Finished "gen_ref", elapsed time 2.835123s.
220706-14:05:25,776 nipype.workflow INFO:
	 [Node] Finished "skull_strip_extern", elapsed time 3.244325s.
220706-14:05:28,661 nipype.workflow INFO:
	 [Node] Finished "trunc_mov", elapsed time 8.552819s.

Thanks!

[effigies]

Hi, I won't get to this this week. I'm aiming for early next week.

[effigies]

I'm not 100% sure why you're seeing the error you are, but I think if we try to get back closer to using the existing FreeSurfer tooling except for the specific places it needs to change, we might fix the bug for free.

[pcamach2]

@effigies, thank you for the review and suggestions! I incorporated most of these, but I'm getting an unusual error in the CircleCI test for ds005 during the fix_surfs:

220804-17:22:08,821 nipype.workflow INFO:
	 [MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 3.80/4.00, Free processors: 1/2.
                     Currently running:
                       * _fix_surfs1
220804-17:22:08,824 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.077021s.
220804-17:22:08,824 nipype.workflow WARNING:
	 Storing result file without outputs
220804-17:22:08,825 nipype.workflow WARNING:
	 [Node] Error on "_fix_surfs1" (/tmp/ds005/work/smriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1)
220804-17:22:08,898 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/tmp/ds005/work/smriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
220804-17:22:08,905 nipype.workflow ERROR:
	 Node _fix_surfs1 failed to run on host 58d564e5dac2.
220804-17:22:08,905 nipype.workflow ERROR:
	 Saving crash info to /tmp/ds005/derivatives/smriprep/sub-01/log/20220804-171742_faed60b5-0084-4efb-b4d1-428c0d848077/crash-20220804-172208-smriprep-_fix_surfs1-6e52b9e6-3e9a-4eff-a665-431cdb03c336.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _fix_surfs1.

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 398, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/smriprep/interfaces/surf.py", line 86, in _run_interface
    self._results["out_file"] = normalize_surfs(
  File "/opt/conda/lib/python3.8/site-packages/smriprep/interfaces/surf.py", line 116, in normalize_surfs
    pointset.meta.pop(f"VolGeom{XYZC}_{RAS}", None)
AttributeError: 'GiftiMetaData' object has no attribute 'pop'

Has this popped up for any other tests with FreeSurfer 7.2?

Thanks!

[effigies]

Ah, we need a newer nibabel. I think 4.0.1.

[pcamach2]

I think the current version of nibabel is 4.0.1 in the Docker image per the build test on CircleCI - https://app.circleci.com/pipelines/github/nipreps/smriprep/468/workflows/ccc25458-5e46-4959-b915-b2853b184b3d/jobs/2232?invite=true#step-107-561 - is there a different python environment that needs to be updated to resolve the errors in the ds005 test?

[pcamach2]

@effigies, I must be missing something simple, but I have not been able to resolve this error in CircleCI testing:

#!/bin/bash -eo pipefail
bash /tmp/src/smriprep/.circleci/ds005_run.sh --write-graph

^@^@Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/smriprep/__main__.py", line 31, in <module>
    main()
  File "/opt/conda/lib/python3.8/site-packages/smriprep/cli/run.py", line 30, in main
    return build_opts(opts)
  File "/opt/conda/lib/python3.8/site-packages/smriprep/cli/run.py", line 336, in build_opts
    raise RuntimeError(
RuntimeError: ERROR: a valid license file is required for FreeSurfer to run. sMRIPrep looked for an existing license file at several paths, in this order: 1) command line argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html

Exited with code exit status 1

CircleCI received exit code 1

[effigies]

Ah, I'm really sorry about the slow response times. I think I saw this in the middle of something else and then the notification got buried. Do you want help resolving merge conflicts?

[pcamach2]

No worries! Any help with the merge conflicts would be great, thanks!

[effigies]

@pcamach2 Sorry I haven't been able to give this the attention it deserves. I want to check in with whether the --fs-no-resume option introduced in https://github.com/nipreps/smriprep/pull/393 will solve your problems, in the sense of allowing FastSurfer outputs to be used?

[pcamach2]

@effigies, no worries! A lot has been updated for both toolkits in the meantime, so I processed a dataset with the latest FastSurfer (v2.2.0) and then used it as an input for sMRIPrep v0.15.0 with the --fs-no-resume argument as you suggested. However, it fails during the midthickness workflow:

$ SINGULARITYENV_MPLCONFIGDIR=/work_dir singularity run --cleanenv -B BICpipeline/beta/testing/PROJECT/bids:/data,./scratch:/work_dir,/home/pcamach2/dev/singularity/license.txt:/opt/freesurfer/license.txt smriprep-v0.15.0.sif /data/sourcedata /data/derivatives/smriprep --fs-license-file /opt/freesurfer/license.txt --fs-subjects-dir /data/derivatives/fastsurfer --fs-no-resume  participant --participant_label PROJECT107
240322-22:30:49,789 nipype.workflow Level 25:
	 
    Running sMRIPrep version 0.15.0:
      * BIDS dataset path: /data/sourcedata.
      * Participant list: ['PROJECT107'].
      * Run identifier: 20240322-223049_9f89222c-f85f-4898-b250-c2a53be624e6.

    Spatial References: <none>.
    
240322-22:30:55,71 nipype.workflow INFO:
	 ANAT Stage 1: Adding template workflow
240322-22:30:55,323 nipype.workflow INFO:
	 ANAT Stage 2: Preparing brain extraction workflow
240322-22:30:57,72 nipype.workflow INFO:
	 ANAT Stage 3: Preparing segmentation workflow
240322-22:30:57,75 nipype.workflow INFO:
	 ANAT Stage 5: Preparing surface reconstruction workflow
240322-22:30:57,89 nipype.workflow INFO:
	 ANAT Stage 6: Preparing mask refinement workflow
240322-22:30:57,91 nipype.workflow INFO:
	 ANAT No T2w images provided - skipping Stage 7
240322-22:30:57,91 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
240322-22:30:57,102 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
240322-22:30:57,107 nipype.workflow INFO:
	 ANAT Stage 8a: Creating cortical ribbon mask
240322-22:30:57,110 nipype.workflow INFO:
	 ANAT Stage 9: Creating fsLR registration sphere
240322-22:30:57,113 nipype.workflow INFO:
	 ANAT Stage 10: Creating MSM-Sulc registration sphere
240322-22:31:00,190 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 0.15.0
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.8.6
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset. The T1w image was corrected for intensity
non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.5.1
[@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL (version unknown), RRID:SCR_002823, @fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 7.3.2,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


240322-22:31:05,747 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/res_tmpl".
240322-22:31:05,748 nipype.workflow INFO:
	 [Node] Executing "res_tmpl" <niworkflows.interfaces.nibabel.RegridToZooms>
240322-22:31:05,874 nipype.workflow INFO:
	 [Node] Finished "res_tmpl", elapsed time 0.117542s.
240322-22:31:05,874 nipype.workflow WARNING:
	 Storing result file without outputs
240322-22:31:05,875 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl" (/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/res_tmpl)
240322-22:31:07,379 nipype.workflow ERROR:
	 Node res_tmpl failed to run on host BI-paul-thinkpad.
240322-22:31:07,380 nipype.workflow ERROR:
	 Saving crash info to /data/derivatives/smriprep/smriprep/sub-PROJECT107/log/20240322-223049_9f89222c-f85f-4898-b250-c2a53be624e6/crash-20240322-223107-smriprep-res_tmpl-467f74f4-82bf-4ee6-9558-573728fc6a98.txt
Traceback (most recent call last):
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node res_tmpl.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/niworkflows/interfaces/nibabel.py", line 314, in _run_interface
	    resample_by_spacing(
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/niworkflows/utils/images.py", line 255, in resample_by_spacing
	    data = gaussian_filter(in_file.get_fdata(), smooth)
	                           ^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
	    data = np.asanyarray(self._dataobj, dtype=dtype)
	           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 457, in __array__
	    arr = self._get_scaled(dtype=dtype, slicer=())
	          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 424, in _get_scaled
	    scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
	                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 394, in _get_unscaled
	    return array_from_file(
	           ^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/smriprep/lib/python3.11/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
	    raise OSError(
	OSError: Expected 64364544 bytes, got 19915580 bytes from object
	 - could the file be damaged?


240322-22:31:07,459 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fs_isrunning" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fs_isrunning".
240322-22:31:07,459 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fs_isrunning".
240322-22:31:07,461 nipype.workflow INFO:
	 [Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function>
240322-22:31:07,462 nipype.workflow INFO:
	 [Node] Finished "fs_isrunning", elapsed time 0.000529s.
240322-22:31:09,512 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fs_base_inputs" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/fs_base_inputs".
240322-22:31:09,514 nipype.workflow INFO:
	 [Node] Executing "fs_base_inputs" <nipype.interfaces.io.FreeSurferSource>
240322-22:31:09,519 nipype.workflow INFO:
	 [Node] Finished "fs_base_inputs", elapsed time 0.005211s.
240322-22:31:09,521 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/get_surfaces".
240322-22:31:09,522 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240322-22:31:09,525 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.003238s.
240322-22:31:16,162 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240322-22:31:16,163 nipype.workflow INFO:
	 [Node] Executing "_midthickness1" <smriprep.interfaces.freesurfer.MakeMidthickness>
240322-22:31:16,163 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240322-22:31:16,165 nipype.workflow INFO:
	 [Node] Executing "_midthickness0" <smriprep.interfaces.freesurfer.MakeMidthickness>
240322-22:31:17,933 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fsnative2t1w_xfm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/fsnative2t1w_xfm".
240322-22:31:17,933 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fsnative2t1w_xfm".
240322-22:31:17,934 nipype.workflow INFO:
	 [Node] Executing "fsnative2t1w_xfm" <niworkflows.interfaces.freesurfer.PatchedRobustRegister>
240322-22:32:25,109 nipype.workflow INFO:
	 [Node] Finished "fsnative2t1w_xfm", elapsed time 67.172965s.
Captured warning (<class 'UserWarning'>): Reference space not set
240322-22:38:48,134 nipype.workflow INFO:
	 [Node] Finished "_midthickness1", elapsed time 451.969496s.
240322-22:38:48,688 nipype.workflow INFO:
	 [Node] Finished "_midthickness0", elapsed time 452.522994s.
240322-22:38:50,233 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240322-22:38:50,234 nipype.workflow INFO:
	 [Node] Cached "_midthickness0" - collecting precomputed outputs
240322-22:38:50,234 nipype.workflow INFO:
	 [Node] "_midthickness0" found cached.
240322-22:38:50,234 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240322-22:38:50,235 nipype.workflow INFO:
	 [Node] Cached "_midthickness1" - collecting precomputed outputs
240322-22:38:50,235 nipype.workflow INFO:
	 [Node] "_midthickness1" found cached.
240322-22:38:51,479 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.save_midthickness" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/save_midthickness".
240322-22:38:51,483 nipype.workflow INFO:
	 [Node] Executing "save_midthickness" <nipype.interfaces.io.DataSink>
240322-22:38:51,508 nipype.workflow INFO:
	 [Node] Finished "save_midthickness", elapsed time 0.024986s.
240322-22:38:53,479 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.sync" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/sync".
240322-22:38:53,481 nipype.workflow INFO:
	 [Node] Executing "sync" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:53,482 nipype.workflow INFO:
	 [Node] Finished "sync", elapsed time 0.000458s.
240322-22:38:55,489 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_surface_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/get_surfaces".
240322-22:38:55,489 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/get_surfaces".
240322-22:38:55,489 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_spheres_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/get_surfaces".
240322-22:38:55,491 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:55,492 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,492 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:55,494 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.002157s.
240322-22:38:55,495 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.00197s.
240322-22:38:55,496 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/segs_to_native_aseg/fs_datasource".
240322-22:38:55,497 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,498 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_reports_wf.recon_report" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_reports_wf/recon_report".
240322-22:38:55,498 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.006057s.
240322-22:38:55,498 nipype.workflow INFO:
	 [Node] Executing "recon_report" <smriprep.interfaces.reports.FSSurfaceReport>
240322-22:38:55,500 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_surface_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/get_surfaces".
240322-22:38:55,501 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.utility.wrappers.Function>
240322-22:38:55,502 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.000615s.
240322-22:38:55,502 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.004462s.
240322-22:38:55,503 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/get_surfaces".
240322-22:38:55,504 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aseg/fs_datasource".
240322-22:38:55,504 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,505 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,507 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.003351s.
240322-22:38:55,509 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aparc_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aparc_aseg/fs_datasource".
240322-22:38:55,510 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240322-22:38:55,511 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.005807s.
240322-22:38:55,513 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.003306s.
240322-22:39:01,485 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:01,485 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:01,486 nipype.workflow INFO:
	 [Node] Executing "_fs2gii0" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,486 nipype.workflow INFO:
	 [Node] Executing "_fs2gii1" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,616 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:01,617 nipype.workflow INFO:
	 [Node] Executing "_fs2gii2" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,620 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
240322-22:39:01,621 nipype.workflow INFO:
	 [Node] Executing "_fs2gii4" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,624 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:01,625 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
240322-22:39:01,626 nipype.workflow INFO:
	 [Node] Executing "_fs2gii0" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,626 nipype.workflow INFO:
	 [Node] Executing "_fs2gii5" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:01,646 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:01,648 nipype.workflow INFO:
	 [Node] Executing "_fs2gii3" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,111 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:02,112 nipype.workflow INFO:
	 [Node] Executing "_fs2gii1" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,123 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:02,124 nipype.workflow INFO:
	 [Node] Executing "_fs2gii2" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,130 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:02,132 nipype.workflow INFO:
	 [Node] Executing "_fs2gii3" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,204 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:02,206 nipype.workflow INFO:
	 [Node] Executing "_fs2gii0" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,231 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:02,233 nipype.workflow INFO:
	 [Node] Executing "_fs2gii1" <nipype.interfaces.freesurfer.utils.MRIsConvert>
240322-22:39:02,538 nipype.workflow INFO:
	 [Node] Finished "_fs2gii1", elapsed time 1.051215s.
240322-22:39:02,634 nipype.workflow INFO:
	 [Node] Finished "_fs2gii3", elapsed time 0.983534s.
240322-22:39:02,644 nipype.workflow INFO:
	 [Node] Finished "_fs2gii0", elapsed time 1.016431s.
240322-22:39:02,650 nipype.workflow INFO:
	 [Node] Finished "_fs2gii5", elapsed time 1.021706s.
240322-22:39:02,667 nipype.workflow INFO:
	 [Node] Finished "_fs2gii4", elapsed time 1.043802s.
240322-22:39:03,5 nipype.workflow INFO:
	 [Node] Finished "_fs2gii2", elapsed time 1.3857300000000001s.
240322-22:39:03,57 nipype.workflow INFO:
	 [Node] Finished "_fs2gii3", elapsed time 0.922497s.
240322-22:39:03,88 nipype.workflow INFO:
	 [Node] Finished "_fs2gii0", elapsed time 1.60118s.
240322-22:39:03,108 nipype.workflow INFO:
	 [Node] Finished "_fs2gii0", elapsed time 0.900182s.
240322-22:39:03,136 nipype.workflow INFO:
	 [Node] Finished "_fs2gii1", elapsed time 0.901023s.
240322-22:39:03,265 nipype.workflow INFO:
	 [Node] Finished "_fs2gii1", elapsed time 1.150844s.
240322-22:39:03,441 nipype.workflow INFO:
	 [Node] Finished "_fs2gii2", elapsed time 1.315556s.
240322-22:39:03,544 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:03,545 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:03,545 nipype.workflow INFO:
	 [Node] Cached "_fs2gii0" - collecting precomputed outputs
240322-22:39:03,545 nipype.workflow INFO:
	 [Node] "_fs2gii0" found cached.
240322-22:39:03,546 nipype.workflow INFO:
	 [Node] Cached "_fs2gii0" - collecting precomputed outputs
240322-22:39:03,546 nipype.workflow INFO:
	 [Node] "_fs2gii0" found cached.
240322-22:39:03,546 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Cached "_fs2gii1" - collecting precomputed outputs
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] "_fs2gii1" found cached.
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Cached "_fs2gii1" - collecting precomputed outputs
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:03,547 nipype.workflow INFO:
	 [Node] "_fs2gii1" found cached.
240322-22:39:03,548 nipype.workflow INFO:
	 [Node] Cached "_fs2gii2" - collecting precomputed outputs
240322-22:39:03,548 nipype.workflow INFO:
	 [Node] "_fs2gii2" found cached.
240322-22:39:03,549 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:03,549 nipype.workflow INFO:
	 [Node] Cached "_fs2gii3" - collecting precomputed outputs
240322-22:39:03,549 nipype.workflow INFO:
	 [Node] "_fs2gii3" found cached.
240322-22:39:03,550 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
240322-22:39:03,551 nipype.workflow INFO:
	 [Node] Cached "_fs2gii4" - collecting precomputed outputs
240322-22:39:03,551 nipype.workflow INFO:
	 [Node] "_fs2gii4" found cached.
240322-22:39:03,551 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
240322-22:39:03,552 nipype.workflow INFO:
	 [Node] Cached "_fs2gii5" - collecting precomputed outputs
240322-22:39:03,552 nipype.workflow INFO:
	 [Node] "_fs2gii5" found cached.
240322-22:39:05,245 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii2".
240322-22:39:05,246 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii2" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,272 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:05,273 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii0" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,319 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:05,320 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii1" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,506 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii0".
240322-22:39:05,507 nipype.workflow INFO:
	 [Node] Cached "_fs2gii0" - collecting precomputed outputs
240322-22:39:05,507 nipype.workflow INFO:
	 [Node] "_fs2gii0" found cached.
240322-22:39:05,507 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii1".
240322-22:39:05,508 nipype.workflow INFO:
	 [Node] Cached "_fs2gii1" - collecting precomputed outputs
240322-22:39:05,508 nipype.workflow INFO:
	 [Node] "_fs2gii1" found cached.
240322-22:39:05,508 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii2".
240322-22:39:05,509 nipype.workflow INFO:
	 [Node] Cached "_fs2gii2" - collecting precomputed outputs
240322-22:39:05,509 nipype.workflow INFO:
	 [Node] "_fs2gii2" found cached.
240322-22:39:05,509 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fs2gii/mapflow/_fs2gii3".
240322-22:39:05,510 nipype.workflow INFO:
	 [Node] Cached "_fs2gii3" - collecting precomputed outputs
240322-22:39:05,510 nipype.workflow INFO:
	 [Node] "_fs2gii3" found cached.
240322-22:39:05,533 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii3".
240322-22:39:05,534 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii3" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,535 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:05,536 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii1" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,541 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:05,542 nipype.workflow INFO:
	 [Node] Executing "_morphs2gii0" <smriprep.interfaces.freesurfer.MRIsConvertData>
240322-22:39:05,856 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii2", elapsed time 0.608711s.
240322-22:39:05,916 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii0", elapsed time 0.641329s.
240322-22:39:05,916 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii1", elapsed time 0.594376s.
240322-22:39:06,72 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii3", elapsed time 0.536187s.
240322-22:39:06,72 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii1", elapsed time 0.534703s.
240322-22:39:06,87 nipype.workflow INFO:
	 [Node] Finished "_morphs2gii0", elapsed time 0.543845s.
240322-22:39:07,565 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:07,566 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs2" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:08,57 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs2", elapsed time 0.490073s.
240322-22:39:09,569 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:09,578 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:09,619 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:09,619 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:09,621 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs2" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:09,621 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs3" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:09,961 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs2", elapsed time 0.339545s.
240322-22:39:10,68 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
240322-22:39:10,68 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs5" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,107 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:10,108 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,140 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:10,140 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,147 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:10,148 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:10,171 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.591632s.
240322-22:39:10,200 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs3", elapsed time 0.578916s.
240322-22:39:10,374 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs5", elapsed time 0.305434s.
240322-22:39:10,443 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.302553s.
240322-22:39:10,462 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.352803s.
240322-22:39:10,464 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:10,465 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii0" - collecting precomputed outputs
240322-22:39:10,465 nipype.workflow INFO:
	 [Node] "_morphs2gii0" found cached.
240322-22:39:10,465 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii1" - collecting precomputed outputs
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] "_morphs2gii1" found cached.
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii2".
240322-22:39:10,466 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii2" - collecting precomputed outputs
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] "_morphs2gii2" found cached.
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii3".
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii3" - collecting precomputed outputs
240322-22:39:10,467 nipype.workflow INFO:
	 [Node] "_morphs2gii3" found cached.
240322-22:39:10,494 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.34468s.
240322-22:39:10,937 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii0".
240322-22:39:10,937 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii0" - collecting precomputed outputs
240322-22:39:10,937 nipype.workflow INFO:
	 [Node] "_morphs2gii0" found cached.
240322-22:39:10,938 nipype.workflow INFO:
	 [Node] Setting-up "_morphs2gii1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/morphs2gii/mapflow/_morphs2gii1".
240322-22:39:10,938 nipype.workflow INFO:
	 [Node] Cached "_morphs2gii1" - collecting precomputed outputs
240322-22:39:10,938 nipype.workflow INFO:
	 [Node] "_morphs2gii1" found cached.
240322-22:39:11,431 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:11,432 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs3" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:11,437 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
240322-22:39:11,438 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs4" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:11,440 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:11,441 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:11,736 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs3", elapsed time 0.303252s.
240322-22:39:11,741 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs4", elapsed time 0.302262s.
240322-22:39:11,749 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.307808s.
240322-22:39:12,388 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:12,389 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240322-22:39:12,690 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.300547s.
240322-22:39:13,535 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240322-22:39:13,536 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs2" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs2" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_spheres_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs3" - collecting precomputed outputs
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] "_fix_surfs3" found cached.
240322-22:39:13,537 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs2" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs2" found cached.
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs3" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs3" found cached.
240322-22:39:13,538 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs4" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs4" - collecting precomputed outputs
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] "_fix_surfs4" found cached.
240322-22:39:13,539 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs5" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
240322-22:39:13,540 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs5" - collecting precomputed outputs
240322-22:39:13,540 nipype.workflow INFO:
	 [Node] "_fix_surfs5" found cached.
240322-22:39:14,490 nipype.workflow INFO:
	 [Node] Finished "recon_report", elapsed time 18.991506s.
240322-22:39:15,978 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc1".
240322-22:39:15,978 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc0".
240322-22:39:15,979 nipype.workflow INFO:
	 [Node] Executing "_invert_sulc1" <smriprep.interfaces.gifti.MetricMath>
240322-22:39:15,979 nipype.workflow INFO:
	 [Node] Executing "_invert_sulc0" <smriprep.interfaces.gifti.MetricMath>
240322-22:39:15,997 nipype.workflow INFO:
	 [Node] Finished "_invert_sulc1", elapsed time 0.017401s.
240322-22:39:16,0 nipype.workflow INFO:
	 [Node] Finished "_invert_sulc0", elapsed time 0.020199s.
240322-22:39:17,641 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc0".
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] Cached "_invert_sulc0" - collecting precomputed outputs
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] "_invert_sulc0" found cached.
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] Setting-up "_invert_sulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc1".
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] Cached "_invert_sulc1" - collecting precomputed outputs
240322-22:39:17,642 nipype.workflow INFO:
	 [Node] "_invert_sulc1" found cached.
240322-22:39:20,414 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject1".
240322-22:39:20,415 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject0".
240322-22:39:20,416 nipype.workflow INFO:
	 [Node] Executing "_project_unproject1" <smriprep.interfaces.workbench.SurfaceSphereProjectUnproject>
240322-22:39:20,416 nipype.workflow INFO:
	 [Node] Executing "_project_unproject0" <smriprep.interfaces.workbench.SurfaceSphereProjectUnproject>
240322-22:39:22,490 nipype.workflow INFO:
	 [Node] Finished "_project_unproject0", elapsed time 1.78163s.
240322-22:39:22,518 nipype.workflow INFO:
	 [Node] Finished "_project_unproject1", elapsed time 1.768811s.
240322-22:39:23,489 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject0".
240322-22:39:23,490 nipype.workflow INFO:
	 [Node] Cached "_project_unproject0" - collecting precomputed outputs
240322-22:39:23,490 nipype.workflow INFO:
	 [Node] "_project_unproject0" found cached.
240322-22:39:23,490 nipype.workflow INFO:
	 [Node] Setting-up "_project_unproject1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fsLR_reg_wf/project_unproject/mapflow/_project_unproject1".
240322-22:39:23,491 nipype.workflow INFO:
	 [Node] Cached "_project_unproject1" - collecting precomputed outputs
240322-22:39:23,491 nipype.workflow INFO:
	 [Node] "_project_unproject1" found cached.
240322-22:39:33,485 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240322-22:39:33,485 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240322-22:39:33,486 nipype.workflow INFO:
	 [Node] Executing "_regress_affine1" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240322-22:39:33,486 nipype.workflow INFO:
	 [Node] Executing "_regress_affine0" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240322-22:39:33,828 nipype.workflow INFO:
	 [Node] Finished "_regress_affine0", elapsed time 0.20802s.
240322-22:39:33,833 nipype.workflow INFO:
	 [Node] Finished "_regress_affine1", elapsed time 0.212368s.
240322-22:39:35,499 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240322-22:39:35,500 nipype.workflow INFO:
	 [Node] Cached "_regress_affine0" - collecting precomputed outputs
240322-22:39:35,500 nipype.workflow INFO:
	 [Node] "_regress_affine0" found cached.
240322-22:39:35,500 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240322-22:39:35,501 nipype.workflow INFO:
	 [Node] Cached "_regress_affine1" - collecting precomputed outputs
240322-22:39:35,501 nipype.workflow INFO:
	 [Node] "_regress_affine1" found cached.
240322-22:39:39,498 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240322-22:39:39,499 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240322-22:39:39,500 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine0" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240322-22:39:39,500 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine1" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240322-22:39:40,53 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine0", elapsed time 0.428945s.
240322-22:39:40,83 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine1", elapsed time 0.444635s.
240322-22:39:41,510 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240322-22:39:41,511 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine0" - collecting precomputed outputs
240322-22:39:41,511 nipype.workflow INFO:
	 [Node] "_apply_surface_affine0" found cached.
240322-22:39:41,512 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240322-22:39:41,513 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine1" - collecting precomputed outputs
240322-22:39:41,513 nipype.workflow INFO:
	 [Node] "_apply_surface_affine1" found cached.
240322-22:39:45,501 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240322-22:39:45,501 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240322-22:39:45,502 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere0" <smriprep.interfaces.workbench.SurfaceModifySphere>
240322-22:39:45,502 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere1" <smriprep.interfaces.workbench.SurfaceModifySphere>
240322-22:39:46,87 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere0", elapsed time 0.443699s.
240322-22:39:46,89 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere1", elapsed time 0.444591s.
240322-22:39:47,501 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240322-22:39:47,502 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere0" - collecting precomputed outputs
240322-22:39:47,502 nipype.workflow INFO:
	 [Node] "_modify_sphere0" found cached.
240322-22:39:47,502 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240322-22:39:47,503 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere1" - collecting precomputed outputs
240322-22:39:47,503 nipype.workflow INFO:
	 [Node] "_modify_sphere1" found cached.
240322-22:39:51,500 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240322-22:39:51,500 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240322-22:39:51,502 nipype.workflow INFO:
	 [Node] Executing "_msmsulc0" <smriprep.interfaces.msm.MSM>
240322-22:39:51,502 nipype.workflow INFO:
	 [Node] Executing "_msmsulc1" <smriprep.interfaces.msm.MSM>
240322-23:02:37,720 nipype.workflow INFO:
	 [Node] Finished "_msmsulc1", elapsed time 1366.217513s.
240322-23:02:41,830 nipype.workflow INFO:
	 [Node] Finished "_msmsulc0", elapsed time 1370.327796s.
240322-23:02:43,641 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240322-23:02:43,645 nipype.workflow INFO:
	 [Node] Cached "_msmsulc0" - collecting precomputed outputs
240322-23:02:43,645 nipype.workflow INFO:
	 [Node] "_msmsulc0" found cached.
240322-23:02:43,645 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240322-23:02:43,649 nipype.workflow INFO:
	 [Node] Cached "_msmsulc1" - collecting precomputed outputs
240322-23:02:43,649 nipype.workflow INFO:
	 [Node] "_msmsulc1" found cached.
240322-23:02:51,556 nipype.workflow ERROR:
	 could not run node: smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl
Preprocessing did not finish successfully. Errors occurred while processing data from participants: PROJECT107 (1). Check the HTML reports for details.

[effigies]

Looks like midthickness worked, but templateflow failed to download the whole file either during image creation or at runtime.

[pcamach2]

Ah, my mistake. The midthickness issue popped up when I used output from an older version of FastSurfer (version < 2.X).

I pulled a local copy of the templates with datalad and the workflow completes now.

$ SINGULARITYENV_TEMPLATEFLOW_HOME=/templateflow SINGULARITYENV_MPLCONFIGDIR=/work_dir singularity run --cleanenv -B BICpipeline/beta/testing/PROJECT/bids:/data,./templateflow:/templateflow,/home/pcamach2/dev/singularity/license.txt:/opt/freesurfer/license.txt smriprep-v0.15.0.sif /data/sourcedata /data/derivatives/smriprep --fs-license-file /opt/freesurfer/license.txt --fs-subjects-dir /data/derivatives/fastsurfer --fs-no-resume  participant --participant_label PROJECT107
240323-15:32:46,26 nipype.workflow Level 25:
	 
    Running sMRIPrep version 0.15.0:
      * BIDS dataset path: /data/sourcedata.
      * Participant list: ['PROJECT107'].
      * Run identifier: 20240323-153245_05a2bfa8-c5dc-44c6-bee0-cab90fa6b1ad.

    Spatial References: <none>.
    
240323-15:32:51,507 nipype.workflow INFO:
	 ANAT Stage 1: Adding template workflow
240323-15:32:51,817 nipype.workflow INFO:
	 ANAT Stage 2: Preparing brain extraction workflow
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 32.4M/32.4M [00:01<00:00, 18.6MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 2.59M/2.59M [00:00<00:00, 7.40MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████| 265k/265k [00:00<00:00, 2.18MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-WM_probseg.nii.gz
100%|█████████████████████████████████████████████████████████████████████████████████████████████████| 4.06M/4.06M [00:00<00:00, 13.7MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BS_probseg.nii.gz
100%|███████████████████████████████████████████████████████████████████████████████████████████████████| 447k/447k [00:00<00:00, 3.50MB/s]
240323-15:32:57,810 nipype.workflow INFO:
	 ANAT Stage 3: Preparing segmentation workflow
240323-15:32:57,814 nipype.workflow INFO:
	 ANAT Stage 5: Preparing surface reconstruction workflow
240323-15:32:57,827 nipype.workflow INFO:
	 ANAT Stage 6: Preparing mask refinement workflow
240323-15:32:57,829 nipype.workflow INFO:
	 ANAT No T2w images provided - skipping Stage 7
240323-15:32:57,829 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
240323-15:32:57,841 nipype.workflow INFO:
	 ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
240323-15:32:57,845 nipype.workflow INFO:
	 ANAT Stage 8a: Creating cortical ribbon mask
240323-15:32:57,848 nipype.workflow INFO:
	 ANAT Stage 9: Creating fsLR registration sphere
240323-15:32:57,850 nipype.workflow INFO:
	 ANAT Stage 10: Creating MSM-Sulc registration sphere
240323-15:33:00,875 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 0.15.0
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.8.6
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset. The T1w image was corrected for intensity
non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.5.1
[@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL (version unknown), RRID:SCR_002823, @fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 7.3.2,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


240323-15:33:04,40 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.full_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/full_wm".
240323-15:33:04,40 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.full_wm".
240323-15:33:04,49 nipype.workflow INFO:
	 [Node] Executing "full_wm" <nipype.interfaces.utility.wrappers.Function>
240323-15:33:04,75 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.lap_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/lap_tmpl".
240323-15:33:04,75 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.lap_tmpl".
240323-15:33:04,76 nipype.workflow INFO:
	 [Node] Executing "lap_tmpl" <nipype.interfaces.ants.utils.ImageMath>
240323-15:33:04,123 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.res_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/res_tmpl".
240323-15:33:04,124 nipype.workflow INFO:
	 [Node] Executing "res_tmpl" <niworkflows.interfaces.nibabel.RegridToZooms>
240323-15:33:04,374 nipype.workflow INFO:
	 [Node] Finished "full_wm", elapsed time 0.322995s.
240323-15:33:04,979 nipype.workflow INFO:
	 [Node] Finished "res_tmpl", elapsed time 0.853718s.
240323-15:33:07,666 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fs_isrunning" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fs_isrunning".
240323-15:33:07,668 nipype.workflow INFO:
	 [Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function>
240323-15:33:07,669 nipype.workflow INFO:
	 [Node] Finished "fs_isrunning", elapsed time 0.000589s.
240323-15:33:09,731 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.fs_base_inputs" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/fs_base_inputs".
240323-15:33:09,733 nipype.workflow INFO:
	 [Node] Executing "fs_base_inputs" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:09,733 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/get_surfaces".
240323-15:33:09,734 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:09,739 nipype.workflow INFO:
	 [Node] Finished "fs_base_inputs", elapsed time 0.005764s.
240323-15:33:09,739 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.005142s.
240323-15:33:10,281 nipype.workflow INFO:
	 [Node] Finished "lap_tmpl", elapsed time 6.109642s.
240323-15:33:11,679 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.mrg_tmpl" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/mrg_tmpl".
240323-15:33:11,679 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.mrg_tmpl".
240323-15:33:11,680 nipype.workflow INFO:
	 [Node] Executing "mrg_tmpl" <nipype.interfaces.utility.base.Merge>
240323-15:33:11,681 nipype.workflow INFO:
	 [Node] Finished "mrg_tmpl", elapsed time 0.000157s.
240323-15:33:16,410 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240323-15:33:16,410 nipype.workflow INFO:
	 [Node] Outdated cache found for "_midthickness1".
240323-15:33:16,421 nipype.workflow INFO:
	 [Node] Executing "_midthickness1" <smriprep.interfaces.freesurfer.MakeMidthickness>
240323-15:33:16,421 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240323-15:33:16,422 nipype.workflow INFO:
	 [Node] Outdated cache found for "_midthickness0".
240323-15:33:16,423 nipype.workflow INFO:
	 [Node] Executing "_midthickness0" <smriprep.interfaces.freesurfer.MakeMidthickness>
240323-15:33:16,549 nipype.workflow INFO:
	 [Node] Finished "_midthickness0", elapsed time 0.124941s.
240323-15:33:16,556 nipype.workflow INFO:
	 [Node] Finished "_midthickness1", elapsed time 0.135097s.
240323-15:33:20,393 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.midthickness".
240323-15:33:20,396 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness0".
240323-15:33:20,396 nipype.workflow INFO:
	 [Node] Cached "_midthickness0" - collecting precomputed outputs
240323-15:33:20,396 nipype.workflow INFO:
	 [Node] "_midthickness0" found cached.
240323-15:33:20,397 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/midthickness/mapflow/_midthickness1".
240323-15:33:20,397 nipype.workflow INFO:
	 [Node] Cached "_midthickness1" - collecting precomputed outputs
240323-15:33:20,397 nipype.workflow INFO:
	 [Node] "_midthickness1" found cached.
240323-15:33:21,677 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.save_midthickness" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/surface_recon_wf/save_midthickness".
240323-15:33:21,677 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.surface_recon_wf.save_midthickness".
240323-15:33:21,678 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.init_aff" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/init_aff".
240323-15:33:21,680 nipype.workflow INFO:
	 [Node] Executing "save_midthickness" <nipype.interfaces.io.DataSink>
240323-15:33:21,684 nipype.workflow INFO:
	 [Node] Executing "init_aff" <nipype.interfaces.ants.utils.AI>
240323-15:33:21,721 nipype.workflow INFO:
	 [Node] Finished "save_midthickness", elapsed time 0.04123s.
240323-15:33:25,674 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/gifti_morphometrics_wf/get_surfaces".
240323-15:33:25,675 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/segs_to_native_aseg/fs_datasource".
240323-15:33:25,675 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,677 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,683 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.006181s.
240323-15:33:25,683 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.007481s.
240323-15:33:25,686 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_morphometrics_wf.get_surfaces" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_morphometrics_wf/get_surfaces".
240323-15:33:25,686 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_reports_wf.recon_report" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_reports_wf/recon_report".
240323-15:33:25,687 nipype.workflow INFO:
	 [Node] Executing "get_surfaces" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,687 nipype.workflow INFO:
	 [Node] Executing "recon_report" <smriprep.interfaces.reports.FSSurfaceReport>
240323-15:33:25,789 nipype.workflow INFO:
	 [Node] Finished "get_surfaces", elapsed time 0.101639s.
240323-15:33:25,791 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aseg/fs_datasource".
240323-15:33:25,792 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,796 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.003723s.
240323-15:33:25,798 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aparc_aseg.fs_datasource" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aparc_aseg/fs_datasource".
240323-15:33:25,798 nipype.workflow INFO:
	 [Node] Executing "fs_datasource" <nipype.interfaces.io.FreeSurferSource>
240323-15:33:25,803 nipype.workflow INFO:
	 [Node] Finished "fs_datasource", elapsed time 0.003996s.
240323-15:33:32,149 nipype.workflow INFO:
	 [Node] Finished "init_aff", elapsed time 10.464129s.
240323-15:33:33,670 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.norm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/norm".
240323-15:33:33,686 nipype.workflow INFO:
	 [Node] Executing "norm" <niworkflows.interfaces.fixes.FixHeaderRegistration>
240323-15:33:42,230 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240323-15:33:42,230 nipype.workflow INFO:
	 [Node] Outdated cache found for "_fix_surfs0".
240323-15:33:42,241 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs0" <smriprep.interfaces.surf.NormalizeSurf>
240323-15:33:42,316 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240323-15:33:42,317 nipype.workflow INFO:
	 [Node] Outdated cache found for "_fix_surfs1".
240323-15:33:42,318 nipype.workflow INFO:
	 [Node] Executing "_fix_surfs1" <smriprep.interfaces.surf.NormalizeSurf>
240323-15:33:42,559 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0", elapsed time 0.316107s.
240323-15:33:42,627 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1", elapsed time 0.307268s.
240323-15:33:43,461 nipype.workflow INFO:
	 [Node] Finished "recon_report", elapsed time 17.773253s.
240323-15:33:46,266 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.gifti_surface_wf.fix_surfs".
240323-15:33:46,267 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
240323-15:33:46,268 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
240323-15:33:59,685 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240323-15:33:59,686 nipype.workflow INFO:
	 [Node] Outdated cache found for "_regress_affine1".
240323-15:33:59,687 nipype.workflow INFO:
	 [Node] Executing "_regress_affine1" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240323-15:34:00,233 nipype.workflow INFO:
	 [Node] Finished "_regress_affine1", elapsed time 0.172088s.
240323-15:34:02,154 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240323-15:34:02,154 nipype.workflow INFO:
	 [Node] Outdated cache found for "_regress_affine0".
240323-15:34:02,156 nipype.workflow INFO:
	 [Node] Executing "_regress_affine0" <smriprep.interfaces.workbench.SurfaceAffineRegression>
240323-15:34:02,562 nipype.workflow INFO:
	 [Node] Finished "_regress_affine0", elapsed time 0.238096s.
240323-15:34:03,671 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.regress_affine".
240323-15:34:03,673 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine0".
240323-15:34:03,674 nipype.workflow INFO:
	 [Node] Cached "_regress_affine0" - collecting precomputed outputs
240323-15:34:03,674 nipype.workflow INFO:
	 [Node] "_regress_affine0" found cached.
240323-15:34:03,674 nipype.workflow INFO:
	 [Node] Setting-up "_regress_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/regress_affine/mapflow/_regress_affine1".
240323-15:34:03,675 nipype.workflow INFO:
	 [Node] Cached "_regress_affine1" - collecting precomputed outputs
240323-15:34:03,675 nipype.workflow INFO:
	 [Node] "_regress_affine1" found cached.
240323-15:34:07,674 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240323-15:34:07,674 nipype.workflow INFO:
	 [Node] Outdated cache found for "_apply_surface_affine0".
240323-15:34:07,675 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine0" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240323-15:34:07,676 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240323-15:34:07,676 nipype.workflow INFO:
	 [Node] Outdated cache found for "_apply_surface_affine1".
240323-15:34:07,677 nipype.workflow INFO:
	 [Node] Executing "_apply_surface_affine1" <smriprep.interfaces.workbench.SurfaceApplyAffine>
240323-15:34:08,232 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine1", elapsed time 0.459004s.
240323-15:34:08,306 nipype.workflow INFO:
	 [Node] Finished "_apply_surface_affine0", elapsed time 0.494098s.
240323-15:34:09,679 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.apply_surface_affine".
240323-15:34:09,681 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine0".
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine0" - collecting precomputed outputs
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] "_apply_surface_affine0" found cached.
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] Setting-up "_apply_surface_affine1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/apply_surface_affine/mapflow/_apply_surface_affine1".
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] Cached "_apply_surface_affine1" - collecting precomputed outputs
240323-15:34:09,682 nipype.workflow INFO:
	 [Node] "_apply_surface_affine1" found cached.
240323-15:34:13,670 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240323-15:34:13,671 nipype.workflow INFO:
	 [Node] Outdated cache found for "_modify_sphere0".
240323-15:34:13,671 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240323-15:34:13,671 nipype.workflow INFO:
	 [Node] Outdated cache found for "_modify_sphere1".
240323-15:34:13,672 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere0" <smriprep.interfaces.workbench.SurfaceModifySphere>
240323-15:34:13,672 nipype.workflow INFO:
	 [Node] Executing "_modify_sphere1" <smriprep.interfaces.workbench.SurfaceModifySphere>
240323-15:34:14,172 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere1", elapsed time 0.417555s.
240323-15:34:14,177 nipype.workflow INFO:
	 [Node] Finished "_modify_sphere0", elapsed time 0.408467s.
240323-15:34:15,704 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.modify_sphere".
240323-15:34:15,706 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0".
240323-15:34:15,707 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere0" - collecting precomputed outputs
240323-15:34:15,707 nipype.workflow INFO:
	 [Node] "_modify_sphere0" found cached.
240323-15:34:15,707 nipype.workflow INFO:
	 [Node] Setting-up "_modify_sphere1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1".
240323-15:34:15,708 nipype.workflow INFO:
	 [Node] Cached "_modify_sphere1" - collecting precomputed outputs
240323-15:34:15,708 nipype.workflow INFO:
	 [Node] "_modify_sphere1" found cached.
240323-15:34:19,711 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240323-15:34:19,712 nipype.workflow INFO:
	 [Node] Outdated cache found for "_msmsulc0".
240323-15:34:19,712 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240323-15:34:19,712 nipype.workflow INFO:
	 [Node] Outdated cache found for "_msmsulc1".
240323-15:34:19,713 nipype.workflow INFO:
	 [Node] Executing "_msmsulc0" <smriprep.interfaces.msm.MSM>
240323-15:34:19,714 nipype.workflow INFO:
	 [Node] Executing "_msmsulc1" <smriprep.interfaces.msm.MSM>
240323-15:38:50,980 nipype.workflow INFO:
	 [Node] Finished "norm", elapsed time 317.190996s.
240323-15:38:51,699 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.map_wmmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/map_wmmask".
240323-15:38:51,700 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.map_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/map_brainmask".
240323-15:38:51,704 nipype.workflow INFO:
	 [Node] Executing "map_wmmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
240323-15:38:51,705 nipype.workflow INFO:
	 [Node] Executing "map_brainmask" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
240323-15:39:08,543 nipype.workflow INFO:
	 [Node] Finished "map_brainmask", elapsed time 16.687305s.
240323-15:39:08,815 nipype.workflow INFO:
	 [Node] Finished "map_wmmask", elapsed time 17.019473s.
240323-15:39:09,690 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.thr_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/thr_brainmask".
240323-15:39:09,691 nipype.workflow INFO:
	 [Node] Executing "thr_brainmask" <nipype.interfaces.ants.utils.ThresholdImage>
240323-15:39:09,707 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
240323-15:39:09,708 nipype.workflow INFO:
	 [Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
240323-15:39:10,607 nipype.workflow INFO:
	 [Node] Finished "thr_brainmask", elapsed time 0.915399s.
240323-15:39:11,692 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
240323-15:39:11,692 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
240323-15:39:11,694 nipype.workflow INFO:
	 [Node] Executing "dil_brainmask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:39:11,694 nipype.workflow INFO:
	 [Node] Executing "03_pad_mask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:39:12,327 nipype.workflow INFO:
	 [Node] Finished "03_pad_mask", elapsed time 0.632806s.
240323-15:39:12,803 nipype.workflow INFO:
	 [Node] Finished "dil_brainmask", elapsed time 1.108915s.
240323-15:39:13,696 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/get_brainmask".
240323-15:39:13,698 nipype.workflow INFO:
	 [Node] Executing "get_brainmask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:39:14,789 nipype.workflow INFO:
	 [Node] Finished "get_brainmask", elapsed time 1.090463s.
240323-15:39:31,153 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0", elapsed time 21.309572s.
240323-15:39:31,689 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/01_atropos".
240323-15:39:31,690 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
240323-15:39:31,691 nipype.workflow INFO:
	 [Node] Executing "01_atropos" <nipype.interfaces.ants.segmentation.Atropos>
240323-15:39:31,691 nipype.workflow INFO:
	 [Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
240323-15:39:32,662 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0", elapsed time 0.970423s.
240323-15:40:07,97 nipype.workflow INFO:
	 [Node] Finished "01_atropos", elapsed time 35.405753s.
240323-15:40:07,706 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
240323-15:40:07,707 nipype.workflow INFO:
	 [Node] Executing "02_pad_segm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:08,486 nipype.workflow INFO:
	 [Node] Finished "02_pad_segm", elapsed time 0.778429s.
240323-15:40:09,693 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
240323-15:40:09,694 nipype.workflow INFO:
	 [Node] Executing "04_sel_labels" <nipype.interfaces.utility.wrappers.Function>
240323-15:40:09,968 nipype.workflow INFO:
	 [Node] Finished "04_sel_labels", elapsed time 0.27416s.
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/06_get_gm".
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/05_get_wm".
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/10_me_csf".
240323-15:40:12,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
240323-15:40:12,605 nipype.workflow INFO:
	 [Node] Executing "06_get_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:12,605 nipype.workflow INFO:
	 [Node] Executing "10_me_csf" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:12,605 nipype.workflow INFO:
	 [Node] Executing "27_depad_csf" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:12,606 nipype.workflow INFO:
	 [Node] Executing "05_get_wm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:13,193 nipype.workflow INFO:
	 [Node] Finished "27_depad_csf", elapsed time 0.587024s.
240323-15:40:13,888 nipype.workflow INFO:
	 [Node] Finished "05_get_wm", elapsed time 1.281898s.
240323-15:40:13,936 nipype.workflow INFO:
	 [Node] Finished "06_get_gm", elapsed time 1.330852s.
240323-15:40:14,610 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
240323-15:40:14,610 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
240323-15:40:14,611 nipype.workflow INFO:
	 [Node] Executing "07_fill_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:14,612 nipype.workflow INFO:
	 [Node] Executing "09_relabel_wm" <nipype.interfaces.ants.utils.MultiplyImages>
240323-15:40:15,254 nipype.workflow INFO:
	 [Node] Finished "09_relabel_wm", elapsed time 0.64159s.
240323-15:40:15,840 nipype.workflow INFO:
	 [Node] Finished "10_me_csf", elapsed time 3.234402s.
240323-15:40:16,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
240323-15:40:16,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
240323-15:40:16,609 nipype.workflow INFO:
	 [Node] Executing "26_depad_wm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:16,614 nipype.workflow INFO:
	 [Node] Executing "apply_wm_prior" <nipype.interfaces.utility.wrappers.Function>
240323-15:40:17,289 nipype.workflow INFO:
	 [Node] Finished "26_depad_wm", elapsed time 0.678833s.
240323-15:40:17,398 nipype.workflow INFO:
	 [Node] Finished "apply_wm_prior", elapsed time 0.783783s.
240323-15:40:18,610 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/inu_n4_final/mapflow/_inu_n4_final0".
240323-15:40:18,611 nipype.workflow INFO:
	 [Node] Executing "_inu_n4_final0" <nipype.interfaces.ants.segmentation.N4BiasFieldCorrection>
240323-15:40:24,620 nipype.workflow INFO:
	 [Node] Finished "07_fill_gm", elapsed time 10.008911s.
240323-15:40:26,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
240323-15:40:26,612 nipype.workflow INFO:
	 [Node] Executing "08_mult_gm" <nipype.interfaces.ants.utils.MultiplyImages>
240323-15:40:27,441 nipype.workflow INFO:
	 [Node] Finished "08_mult_gm", elapsed time 0.829026s.
240323-15:40:28,623 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/11_add_gm".
240323-15:40:28,625 nipype.workflow INFO:
	 [Node] Executing "11_add_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:30,37 nipype.workflow INFO:
	 [Node] Finished "11_add_gm", elapsed time 1.412401s.
240323-15:40:30,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
240323-15:40:30,610 nipype.workflow INFO:
	 [Node] Executing "12_relabel_gm" <nipype.interfaces.ants.utils.MultiplyImages>
240323-15:40:31,271 nipype.workflow INFO:
	 [Node] Finished "12_relabel_gm", elapsed time 0.65975s.
240323-15:40:32,620 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
240323-15:40:32,620 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
240323-15:40:32,621 nipype.workflow INFO:
	 [Node] Executing "25_depad_gm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:32,621 nipype.workflow INFO:
	 [Node] Executing "13_add_gm_wm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:33,359 nipype.workflow INFO:
	 [Node] Finished "25_depad_gm", elapsed time 0.737597s.
240323-15:40:34,244 nipype.workflow INFO:
	 [Node] Finished "13_add_gm_wm", elapsed time 1.622328s.
240323-15:40:34,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
240323-15:40:34,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
240323-15:40:34,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/merge_tpms".
240323-15:40:34,612 nipype.workflow INFO:
	 [Node] Executing "24_depad_segm" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:34,612 nipype.workflow INFO:
	 [Node] Executing "14_sel_labels2" <nipype.interfaces.utility.wrappers.Function>
240323-15:40:34,614 nipype.workflow INFO:
	 [Node] Executing "merge_tpms" <nipype.interfaces.utility.base.Merge>
240323-15:40:34,614 nipype.workflow INFO:
	 [Node] Finished "merge_tpms", elapsed time 0.000187s.
240323-15:40:34,806 nipype.workflow INFO:
	 [Node] Finished "14_sel_labels2", elapsed time 0.1936s.
240323-15:40:35,329 nipype.workflow INFO:
	 [Node] Finished "24_depad_segm", elapsed time 0.716292s.
240323-15:40:36,608 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/15_add_7".
240323-15:40:36,610 nipype.workflow INFO:
	 [Node] Executing "15_add_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:37,775 nipype.workflow INFO:
	 [Node] Finished "15_add_7", elapsed time 1.164979s.
240323-15:40:38,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/16_me_7".
240323-15:40:38,613 nipype.workflow INFO:
	 [Node] Executing "16_me_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:40,444 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0", elapsed time 21.832634s.
240323-15:40:41,188 nipype.workflow INFO:
	 [Node] Finished "16_me_7", elapsed time 2.5746700000000002s.
240323-15:40:42,609 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/17_comp_7".
240323-15:40:42,610 nipype.workflow INFO:
	 [Node] Executing "17_comp_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:43,936 nipype.workflow INFO:
	 [Node] Finished "17_comp_7", elapsed time 1.325434s.
240323-15:40:44,607 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/18_md_7".
240323-15:40:44,608 nipype.workflow INFO:
	 [Node] Executing "18_md_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:45,942 nipype.workflow INFO:
	 [Node] Finished "18_md_7", elapsed time 1.33344s.
240323-15:40:46,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/19_fill_7".
240323-15:40:46,612 nipype.workflow INFO:
	 [Node] Executing "19_fill_7" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:56,88 nipype.workflow INFO:
	 [Node] Finished "19_fill_7", elapsed time 9.475285s.
240323-15:40:56,613 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
240323-15:40:56,615 nipype.workflow INFO:
	 [Node] Executing "20_add_7_2" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:57,938 nipype.workflow INFO:
	 [Node] Finished "20_add_7_2", elapsed time 1.322305s.
240323-15:40:58,612 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
240323-15:40:58,613 nipype.workflow INFO:
	 [Node] Executing "21_md_7_2" <nipype.interfaces.ants.utils.ImageMath>
240323-15:40:59,927 nipype.workflow INFO:
	 [Node] Finished "21_md_7_2", elapsed time 1.31346s.
240323-15:41:00,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
240323-15:41:00,613 nipype.workflow INFO:
	 [Node] Executing "22_me_7_2" <nipype.interfaces.ants.utils.ImageMath>
240323-15:41:03,189 nipype.workflow INFO:
	 [Node] Finished "22_me_7_2", elapsed time 2.576308s.
240323-15:41:04,611 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
240323-15:41:04,612 nipype.workflow INFO:
	 [Node] Executing "23_depad_mask" <nipype.interfaces.ants.utils.ImageMath>
240323-15:41:05,234 nipype.workflow INFO:
	 [Node] Finished "23_depad_mask", elapsed time 0.621838s.
240323-15:41:06,609 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/msk_conform".
240323-15:41:06,613 nipype.workflow INFO:
	 [Node] Executing "msk_conform" <nipype.interfaces.utility.wrappers.Function>
240323-15:41:06,801 nipype.workflow INFO:
	 [Node] Finished "msk_conform", elapsed time 0.187184s.
240323-15:41:15,364 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/apply_mask/mapflow/_apply_mask0".
240323-15:41:15,365 nipype.workflow INFO:
	 [Node] Executing "_apply_mask0" <niworkflows.interfaces.nibabel.ApplyMask>
240323-15:41:16,319 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0", elapsed time 0.954324s.
Captured warning (<class 'UserWarning'>): Reference space not set
240323-15:41:19,892 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol0".
240323-15:41:19,892 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol1".
240323-15:41:19,893 nipype.workflow INFO:
	 [Node] Executing "_create_wm_distvol0" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,893 nipype.workflow INFO:
	 [Node] Executing "_create_wm_distvol1" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,894 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol1".
240323-15:41:19,895 nipype.workflow INFO:
	 [Node] Executing "_create_pial_distvol1" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,898 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol0".
240323-15:41:19,899 nipype.workflow INFO:
	 [Node] Executing "_create_pial_distvol0" <smriprep.interfaces.workbench.CreateSignedDistanceVolume>
240323-15:41:19,920 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.segs_to_native_aseg.resample" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/segs_to_native_aseg/resample".
240323-15:41:19,923 nipype.workflow INFO:
	 [Node] Executing "resample" <nipype.interfaces.freesurfer.preprocess.ApplyVolTransform>
240323-15:41:21,751 nipype.workflow INFO:
	 [Node] Finished "resample", elapsed time 1.827715s.
240323-15:41:21,753 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aseg.resample" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aseg/resample".
240323-15:41:21,757 nipype.workflow INFO:
	 [Node] Executing "resample" <nipype.interfaces.freesurfer.preprocess.ApplyVolTransform>
240323-15:41:22,124 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.surface_derivatives_wf.segs_to_native_aparc_aseg.resample" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/surface_derivatives_wf/segs_to_native_aparc_aseg/resample".
240323-15:41:23,731 nipype.workflow INFO:
	 [Node] Finished "resample", elapsed time 1.973246s.
240323-15:41:25,523 nipype.interface WARNING:
	 Changing /data/derivatives/smriprep/smriprep/sub-PROJECT107/ses-A/anat/sub-PROJECT107_ses-A_desc-aseg_dseg.nii.gz dtype from float32 to int16
240323-15:41:25,897 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.refinement_wf.refine" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/refinement_wf/refine".
240323-15:41:25,904 nipype.workflow INFO:
	 [Node] Executing "refine" <niworkflows.interfaces.freesurfer.RefineBrainMask>
240323-15:41:26,270 nipype.workflow INFO:
	 [Node] Executing "resample" <nipype.interfaces.freesurfer.preprocess.ApplyVolTransform>
240323-15:41:28,154 nipype.workflow INFO:
	 [Node] Finished "resample", elapsed time 1.881231s.
240323-15:41:29,893 nipype.interface WARNING:
	 Changing /data/derivatives/smriprep/smriprep/sub-PROJECT107/ses-A/anat/sub-PROJECT107_ses-A_desc-aparcaseg_dseg.nii.gz dtype from float32 to int16
240323-15:41:58,916 nipype.workflow INFO:
	 [Node] Finished "refine", elapsed time 33.009822s.
240323-15:41:59,934 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.applyrefined" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/applyrefined".
240323-15:42:00,499 nipype.workflow INFO:
	 [Node] Executing "applyrefined" <nipype.interfaces.fsl.maths.ApplyMask>
240323-15:42:01,871 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.ds_std_volumes_wf.mask_t1w" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/ds_std_volumes_wf/mask_t1w".
240323-15:42:01,874 nipype.workflow INFO:
	 [Node] Executing "mask_t1w" <niworkflows.interfaces.nibabel.ApplyMask>
240323-15:42:03,175 nipype.workflow INFO:
	 [Node] Finished "mask_t1w", elapsed time 1.30036s.
240323-15:42:03,568 nipype.workflow INFO:
	 [Node] Finished "applyrefined", elapsed time 3.067401s.
240323-15:42:03,878 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.fast" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/fast".
240323-15:42:03,881 nipype.workflow INFO:
	 [Node] Executing "fast" <nipype.interfaces.fsl.preprocess.FAST>
240323-15:42:18,490 nipype.workflow INFO:
	 [Node] Finished "_create_wm_distvol0", elapsed time 58.527644s.
240323-15:42:19,514 nipype.workflow INFO:
	 [Node] Finished "_create_wm_distvol1", elapsed time 59.539599s.
240323-15:42:19,869 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol0".
240323-15:42:19,869 nipype.workflow INFO:
	 [Node] Cached "_create_wm_distvol0" - collecting precomputed outputs
240323-15:42:19,870 nipype.workflow INFO:
	 [Node] "_create_wm_distvol0" found cached.
240323-15:42:19,870 nipype.workflow INFO:
	 [Node] Setting-up "_create_wm_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_wm_distvol/mapflow/_create_wm_distvol1".
240323-15:42:19,871 nipype.workflow INFO:
	 [Node] Cached "_create_wm_distvol1" - collecting precomputed outputs
240323-15:42:19,871 nipype.workflow INFO:
	 [Node] "_create_wm_distvol1" found cached.
240323-15:42:28,863 nipype.workflow INFO:
	 [Node] Finished "_create_pial_distvol0", elapsed time 68.885826s.
240323-15:42:30,731 nipype.workflow INFO:
	 [Node] Finished "_create_pial_distvol1", elapsed time 70.775295s.
240323-15:42:31,832 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol0".
240323-15:42:31,832 nipype.workflow INFO:
	 [Node] Cached "_create_pial_distvol0" - collecting precomputed outputs
240323-15:42:31,833 nipype.workflow INFO:
	 [Node] "_create_pial_distvol0" found cached.
240323-15:42:31,833 nipype.workflow INFO:
	 [Node] Setting-up "_create_pial_distvol1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/create_pial_distvol/mapflow/_create_pial_distvol1".
240323-15:42:31,834 nipype.workflow INFO:
	 [Node] Cached "_create_pial_distvol1" - collecting precomputed outputs
240323-15:42:31,834 nipype.workflow INFO:
	 [Node] "_create_pial_distvol1" found cached.
240323-15:42:33,827 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_ribbon_wf.make_ribbon" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_ribbon_wf/make_ribbon".
240323-15:42:33,828 nipype.workflow INFO:
	 [Node] Executing "make_ribbon" <smriprep.interfaces.surf.MakeRibbon>
240323-15:42:34,438 nipype.workflow INFO:
	 [Node] Finished "make_ribbon", elapsed time 0.60952s.
240323-15:43:29,759 nipype.workflow INFO:
	 [Node] Finished "fast", elapsed time 85.877111s.
240323-15:43:29,835 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.lut_t1w_dseg" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/lut_t1w_dseg".
240323-15:43:29,837 nipype.workflow INFO:
	 [Node] Executing "lut_t1w_dseg" <nipype.interfaces.utility.wrappers.Function>
240323-15:43:30,42 nipype.workflow INFO:
	 [Node] Finished "lut_t1w_dseg", elapsed time 0.204572s.
240323-15:43:37,735 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.anat_reports_wf.seg_rpt" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/anat_reports_wf/seg_rpt".
240323-15:43:37,737 nipype.workflow INFO:
	 [Node] Executing "seg_rpt" <niworkflows.interfaces.reportlets.masks.ROIsPlot>
240323-15:43:55,88 nipype.workflow INFO:
	 [Node] Finished "seg_rpt", elapsed time 17.351331s.
240323-15:57:52,574 nipype.workflow INFO:
	 [Node] Finished "_msmsulc0", elapsed time 1412.860192s.
240323-15:58:02,821 nipype.workflow INFO:
	 [Node] Finished "_msmsulc1", elapsed time 1423.105562s.
240323-15:58:03,506 nipype.workflow INFO:
	 [Node] Outdated cache found for "smriprep_wf.single_subject_PROJECT107_wf.anat_preproc_wf.anat_fit_wf.msm_sulc_wf.msmsulc".
240323-15:58:03,509 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc0" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0".
240323-15:58:03,511 nipype.workflow INFO:
	 [Node] Cached "_msmsulc0" - collecting precomputed outputs
240323-15:58:03,511 nipype.workflow INFO:
	 [Node] "_msmsulc0" found cached.
240323-15:58:03,511 nipype.workflow INFO:
	 [Node] Setting-up "_msmsulc1" in "/home/pcamach2/dev/singularity/fastsurfer-smriprep/work/smriprep_wf/single_subject_PROJECT107_wf/anat_preproc_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1".
240323-15:58:03,513 nipype.workflow INFO:
	 [Node] Cached "_msmsulc1" - collecting precomputed outputs
240323-15:58:03,513 nipype.workflow INFO:
	 [Node] "_msmsulc1" found cached.

In my current role, I do not have the throughput to bring this PR up to date. If you know anyone who would be interested in doing so, I would be happy to help. Otherwise, I think we should drop the FastSurfer installation & interface and just add examples of using FastSurfer inputs to the relevant documentation for sMRIPrep/fMRIPrep.

Please let me know what you think! I appreciate the feedback and guidance on this.