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...

@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...

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...

@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...

@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...

@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...

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...

###Environment testing:### - [x] Complete runs of FastSurfer GPU in the Docker version of this container - [x] Complete runs of FastSurfer GPU in the Singularity version of this container...

Any help with integrating this to Nipype would be very much appreciated!

Hi @effigies, no problem! Here is what I have so far: > 1. What does a command-line look like? What inputs does it have, what options does it have? Per...