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Randomly fail when using functions in anat_fit_wf
What happened?
We are running fmriprep within docker for our own subject database (rs-fMRI, T1, T2). The laptop I'm using has M3 chip, 32GB memory, and 12 cores. Some of the subjects pass successfully, but the rest of them failed on different types of nodes:
240427-02:38:36,572 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1
240427-02:38:36,594 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_02_wf.anat_fit_wf.brain_extraction_wf.atropos_wf.24_depad_segm
240427-02:38:36,605 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_13_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol
240427-02:38:36,613 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_14_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol
240427-02:38:36,620 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_18_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol
240427-02:38:36,626 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_18_wf.anat_fit_wf.t2w_template_wf.anat_merge
240427-02:38:36,631 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_11_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
240427-02:38:36,636 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_08_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
240427-02:38:36,640 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_25_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
240427-02:38:36,645 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_28_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.cortribbon
240427-02:38:36,649 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_06_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.parcstats
240427-02:38:36,652 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_15_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.parcstats
240427-02:38:36,656 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_23_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.parcstats
240427-02:38:36,659 nipype.workflow ERROR:
could not run node: fmriprep_23_2_wf.sub_24_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon3
240427-02:38:36,890 nipype.workflow CRITICAL:
fMRIPrep failed: 14 raised. Re-raising first.
240427-02:38:51,253 cli ERROR:
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 01 (1), 02 (1), 06 (1), 08 (1), 11 (1), 13 (1), 14 (1), 15 (1), 18 (2), 23 (1), 24 (1), 25 (1), 28 (1).
I tried running fmriprep on only one subject (subject 14) with two sessions, it failed on a different error.
240430-19:17:18,914 nipype.workflow WARNING:
[Node] Error on "fmriprep_23_2_wf.sub_14_wf.anat_fit_wf.surface_recon_wf.autorecon1" (/scratch/fmriprep_23_2_wf/sub_14_wf/anat_fit_wf/surface_recon_wf/autorecon1)
240430-19:17:20,459 nipype.workflow ERROR:
Node autorecon1 failed to run on host 005abe4ae096.
240430-19:17:20,464 nipype.workflow ERROR:
Saving crash info to /out/sub-14/log/20240430-190529_47e10b7b-b8e4-470a-b82e-8aa193ebf15d/crash-20240430-191720-root-autorecon1-cb641879-36eb-42b0-9e06-aca5f6b0a846.txt
Another attempt fmriprep on only subject 15 with two sessions is successful. Since it failed at the first time, I think it's similar to issue #3220:https://github.com/nipreps/fmriprep/issues/3220#issue-2119212392, but our data is located at Desktop directory of Mac which I believe is not FAT/NTFS.
What command did you use?
fmriprep-docker tDCS_BIDS_test tDCS_BIDS_test_output -w fmriprep_working --omp-nthreads=6 --mem_mb=24000
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=25.0.3 -it -v /Users/jungheeha/Desktop/tDCS_BIDS_test:/data:ro -v /Users/jungheeha/Desktop/tDCS_BIDS_test_output:/out -v /Users/jungheeha/Desktop/fmriprep_working:/scratch nipreps/fmriprep:23.2.1 /data /out participant --omp-nthreads=6 --mem_mb=24000 -w /scratch
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
What version of fMRIPrep are you running?
23.2.1
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
This is the log from the attempt with subject 14 only:
Node Name: fmriprep_23_2_wf.sub_14_wf.anat_fit_wf.surface_recon_wf.autorecon1
File: /out/sub-14/log/20240430-190529_47e10b7b-b8e4-470a-b82e-8aa193ebf15d/crash-20240430-191720-root-autorecon1-cb641879-36eb-42b0-9e06-aca5f6b0a846.txt
Working Directory: /scratch/fmriprep_23_2_wf/sub_14_wf/anat_fit_wf/surface_recon_wf/autorecon1
Inputs:
FLAIR_file:
T1_files:
T2_file:
args:
big_ventricles:
brainstem:
directive: autorecon1
environ: {}
expert:
flags:
hemi:
hippocampal_subfields_T1:
hippocampal_subfields_T2:
hires:
mprage:
mri_aparc2aseg:
mri_ca_label:
mri_ca_normalize:
mri_ca_register:
mri_edit_wm_with_aseg:
mri_em_register:
mri_fill:
mri_mask:
mri_normalize:
mri_pretess:
mri_remove_neck:
mri_segment:
mri_segstats:
mri_tessellate:
mri_watershed:
mris_anatomical_stats:
mris_ca_label:
mris_fix_topology:
mris_inflate:
mris_make_surfaces:
mris_register:
mris_smooth:
mris_sphere:
mris_surf2vol:
mrisp_paint:
openmp: 6
parallel:
steps:
subject_id: recon_all
subjects_dir:
talairach:
use_FLAIR:
use_T2:
xopts:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/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 autorecon1.
Cmdline:
recon-all -autorecon1 -i /scratch/fmriprep_23_2_wf/sub_14_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-14_ses-01_T1w_noise_corrected_ras_template.nii -T2 /data/sub-14/ses-01/anat/sub-14_ses-01_T2w.nii -noskullstrip -noT2pial -noFLAIRpial -openmp 6 -subjid sub-14 -sd /out/sourcedata/freesurfer
Stdout:
fs-check-version --s sub-14 --o /tmp/tmp.OIwy39
Tue Apr 30 19:11:07 UTC 2024
setenv SUBJECTS_DIR /out/sourcedata/freesurfer
cd /scratch/fmriprep_23_2_wf/sub_14_wf/anat_fit_wf/surface_recon_wf/autorecon1
/opt/freesurfer/bin/fs-check-version --s sub-14 --o /tmp/tmp.OIwy39
-rwxrwxr-x 1 root root 18565 Aug 4 2022 /opt/freesurfer/bin/fs-check-version
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
$Id$
Linux 005abe4ae096 6.6.16-linuxkit #1 SMP Fri Feb 16 11:54:02 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
pid 468
Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
Subject does not have a bstampfile, copying /opt/freesurfer/build-stamp.txt
Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /out/sourcedata/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux 005abe4ae096 6.6.16-linuxkit #1 SMP Fri Feb 16 11:54:02 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
/out/sourcedata/freesurfer/sub-14
mri_convert /scratch/fmriprep_23_2_wf/sub_14_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-14_ses-01_T1w_noise_corrected_ras_template.nii /out/sourcedata/freesurfer/sub-14/mri/orig/001.mgz
mri_convert /scratch/fmriprep_23_2_wf/sub_14_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-14_ses-01_T1w_noise_corrected_ras_template.nii /out/sourcedata/freesurfer/sub-14/mri/orig/001.mgz
reading from /scratch/fmriprep_23_2_wf/sub_14_wf/anat_fit_wf/anat_template_wf/anat_merge/sub-14_ses-01_T1w_noise_corrected_ras_template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998126, 0.0459843, -0.0403783)
j_ras = (-0.0317161, 0.952999, 0.301308)
k_ras = (0.052336, -0.299462, 0.952672)
writing to /out/sourcedata/freesurfer/sub-14/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Tue Apr 30 19:11:17 UTC 2024
/out/sourcedata/freesurfer/sub-14
mri_convert --no_scale 1 /data/sub-14/ses-01/anat/sub-14_ses-01_T2w.nii /out/sourcedata/freesurfer/sub-14/mri/orig/T2raw.mgz
mri_convert --no_scale 1 /data/sub-14/ses-01/anat/sub-14_ses-01_T2w.nii /out/sourcedata/freesurfer/sub-14/mri/orig/T2raw.mgz
reading from /data/sub-14/ses-01/anat/sub-14_ses-01_T2w.nii...
TR=4800.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0317161, -0.952999, -0.301308)
j_ras = (0.052336, -0.299462, 0.952672)
k_ras = (0.998126, 0.0459843, -0.0403783)
writing to /out/sourcedata/freesurfer/sub-14/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Tue Apr 30 19:11:34 UTC 2024
Found 1 runs
/out/sourcedata/freesurfer/sub-14/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.
cp /out/sourcedata/freesurfer/sub-14/mri/orig/001.mgz /out/sourcedata/freesurfer/sub-14/mri/rawavg.mgz
mri_info /out/sourcedata/freesurfer/sub-14/mri/rawavg.mgz
rawavg.mgz ========================================
Volume information for /out/sourcedata/freesurfer/sub-14/mri/rawavg.mgz
type: MGH
dimensions: 224 x 220 x 224
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 224.000
dof: 1
xstart: -112.0, xend: 112.0
ystart: -110.0, yend: 110.0
zstart: -112.0, zend: 112.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = 0.9981, y_r = -0.0317, z_r = 0.0523, c_r = 2.7663
: x_a = 0.0460, y_a = 0.9530, z_a = -0.2995, c_a = -11.0132
: x_s = -0.0404, y_s = 0.3013, z_s = 0.9527, c_s = -5.3312
talairach xfm :
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
0.9981 -0.0317 0.0523 -111.3966
0.0460 0.9530 -0.2995 -87.4536
-0.0404 0.3013 0.9527 -140.6519
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform:
0.9981 0.0460 -0.0404 109.5300
-0.0317 0.9530 0.3013 122.1897
0.0523 -0.2995 0.9527 113.6361
0.0000 0.0000 0.0000 1.0000
/out/sourcedata/freesurfer/sub-14
mri_convert /out/sourcedata/freesurfer/sub-14/mri/rawavg.mgz /out/sourcedata/freesurfer/sub-14/mri/orig.mgz --conform
mri_convert /out/sourcedata/freesurfer/sub-14/mri/rawavg.mgz /out/sourcedata/freesurfer/sub-14/mri/orig.mgz --conform
reading from /out/sourcedata/freesurfer/sub-14/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998126, 0.0459843, -0.0403783)
j_ras = (-0.0317161, 0.952999, 0.301308)
k_ras = (0.052336, -0.299462, 0.952672)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram -12222.6 240095 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to /out/sourcedata/freesurfer/sub-14/mri/orig.mgz...
mri_add_xform_to_header -c /out/sourcedata/freesurfer/sub-14/mri/transforms/talairach.xfm /out/sourcedata/freesurfer/sub-14/mri/orig.mgz /out/sourcedata/freesurfer/sub-14/mri/orig.mgz
INFO: extension is mgz
mri_info /out/sourcedata/freesurfer/sub-14/mri/orig.mgz
orig.mgz ========================================
Volume information for /out/sourcedata/freesurfer/sub-14/mri/orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 2.7663
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -11.0132
: x_s = 0.0000, y_s = -1.0000, z_s = -0.0000, c_s = -5.3312
talairach xfm : /out/sourcedata/freesurfer/sub-14/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 130.7663
0.0000 0.0000 1.0000 -139.0132
0.0000 -1.0000 -0.0000 122.6688
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 -0.0000 -0.0000 130.7663
-0.0000 -0.0000 -1.0000 122.6688
0.0000 1.0000 -0.0000 139.0132
-0.0000 -0.0000 -0.0000 1.0000
#--------------------------------------------
#@# Talairach Tue Apr 30 19:11:42 UTC 2024
/out/sourcedata/freesurfer/sub-14/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
/usr/bin/bc
/out/sourcedata/freesurfer/sub-14/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
nIters 1
mri_nu_correct.mni 7.3.2
Linux 005abe4ae096 6.6.16-linuxkit #1 SMP Fri Feb 16 11:54:02 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
Tue Apr 30 19:11:43 UTC 2024
tmpdir is ./tmp.mri_nu_correct.mni.835
cd /out/sourcedata/freesurfer/sub-14/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.835/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_convert ./tmp.mri_nu_correct.mni.835/nu0.mgz orig_nu.mgz --like orig.mgz --conform
mri_convert ./tmp.mri_nu_correct.mni.835/nu0.mgz orig_nu.mgz --like orig.mgz --conform
reading from ./tmp.mri_nu_correct.mni.835/nu0.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, -2.98023e-08)
INFO: transform src into the like-volume: orig.mgz
writing to orig_nu.mgz...
Tue Apr 30 19:14:07 UTC 2024
mri_nu_correct.mni done
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
mv -f /out/sourcedata/freesurfer/sub-14/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /out/sourcedata/freesurfer/sub-14/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
Started at Tue Apr 30 19:14:08 UTC 2024
Ended at Tue Apr 30 19:14:29 UTC 2024
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
7.3.2
--src: orig.mgz src image (geometry).
--trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
--inmni: transforms/talairach.xfm input MNI/XFM transform.
--outlta: transforms/talairach.xfm.lta output LTA.
--s: fsaverage subject name
--ltavox2vox: output LTA as VOX_TO_VOX transform.
LTA read, type : 1
0.98559 0.03697 -0.04689 -0.52249;
-0.02291 1.06278 0.24999 -3.72581;
0.04425 -0.25222 0.99025 -0.46518;
0.00000 0.00000 0.00000 1.00000;
setting subject to fsaverage
Writing LTA to file transforms/talairach.xfm.lta...
lta_convert successful.
/out/sourcedata/freesurfer/sub-14/mri/transforms /out/sourcedata/freesurfer/sub-14/mri
/out/sourcedata/freesurfer/sub-14/mri
#--------------------------------------------
#@# Talairach Failure Detection Tue Apr 30 19:14:31 UTC 2024
/out/sourcedata/freesurfer/sub-14/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6727, pval=0.3663 >= threshold=0.0050)
awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/sourcedata/freesurfer/sub-14/mri/transforms/talairach_avi.log
tal_QC_AZS /out/sourcedata/freesurfer/sub-14/mri/transforms/talairach_avi.log
TalAviQA: 0.97662
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Tue Apr 30 19:14:31 UTC 2024
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
/usr/bin/bc
/out/sourcedata/freesurfer/sub-14/mri
/opt/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
nIters 2
mri_nu_correct.mni 7.3.2
Linux 005abe4ae096 6.6.16-linuxkit #1 SMP Fri Feb 16 11:54:02 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
Tue Apr 30 19:14:32 UTC 2024
tmpdir is ./tmp.mri_nu_correct.mni.1094
cd /out/sourcedata/freesurfer/sub-14/mri
AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.1094/nu0.mgz --dtype uchar
AntsN4BiasFieldCorrectionFs done
mri_binarize --i ./tmp.mri_nu_correct.mni.1094/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.1094/ones.mgz
7.3.2
cwd /out/sourcedata/freesurfer/sub-14/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.1094/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.1094/ones.mgz
sysname Linux
hostname 005abe4ae096
machine x86_64
user root
input ./tmp.mri_nu_correct.mni.1094/nu0.mgz
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.1094/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Starting parallel 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777215 voxels in final mask
Writing output to ./tmp.mri_nu_correct.mni.1094/ones.mgz
Count: 16777215 16777215.000000 16777216 99.999994
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1094/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1094/input.mean.dat
7.3.2
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1094/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1094/input.mean.dat
sysname Linux
hostname 005abe4ae096
machine x86_64
user root
whitesurfname white
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.1094/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.1094/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1094/ones.mgz --i ./tmp.mri_nu_correct.mni.1094/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1094/output.mean.dat
7.3.2
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1094/ones.mgz --i ./tmp.mri_nu_correct.mni.1094/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1094/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1094/output.mean.dat
sysname Linux
hostname 005abe4ae096
machine x86_64
user root
whitesurfname white
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.1094/ones.mgz
Loading ./tmp.mri_nu_correct.mni.1094/nu0.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
Writing to ./tmp.mri_nu_correct.mni.1094/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.1094/nu0.mgz ./tmp.mri_nu_correct.mni.1094/nu0.mgz mul 1.37393233565938209479
Saving result to './tmp.mri_nu_correct.mni.1094/nu0.mgz' (type = MGH ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.1094/nu0.mgz nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.1094/nu0.mgz nu.mgz --like orig.mgz
reading from ./tmp.mri_nu_correct.mni.1094/nu0.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, -2.98023e-08)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 4 seconds.
FIRST_PERCENTILE 0.010000
WM_PERCENTILE 0.900000
MAX_R 50.000000
i1 = 10, i2 = 64
#mri_make_uchar# mapping 24 152 to 3 110 : b -17.3481 m 0.838262 : thresh 20.6954 maxsat 324.896 : nzero 12380809 nsat 0
Tue Apr 30 19:17:17 UTC 2024
mri_nu_correct.mni done
mri_add_xform_to_header -c /out/sourcedata/freesurfer/sub-14/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Tue Apr 30 19:17:18 UTC 2024
/out/sourcedata/freesurfer/sub-14/mri
mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz
upt: Subscript out of range.
Linux 005abe4ae096 6.6.16-linuxkit #1 SMP Fri Feb 16 11:54:02 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-14 exited with ERRORS at Tue Apr 30 19:17:18 UTC 2024
For more details, see the log file /out/sourcedata/freesurfer/sub-14/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Stderr:
Traceback:
RuntimeError: subprocess exited with code 1.
Additional information / screenshots
No response
The only thing I can find about "upt: Subscript out of range." is https://github.com/freesurfer/freesurfer/issues/1042, but uptime is part of our docker images, so that seems unlikely to be the problem. Did you look for errors in /out/sourcedata/freesurfer/sub-14/scripts/recon-all.log?
