Create fmriprep-DARBY-PDK_v24.1.1.yaml

[duettwe]

Bug 3235 - In progress

Creating this repo so I remember where we are next week when this gets worked on again.

[duettwe]

Any ideas here?

250129-00:30:38,134 nipype.workflow IMPORTANT:
	 Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
2025-01-29 00:30:38,134 [IMPORTANT] Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
cp: cannot overwrite non-directory '/OUTPUTS/HTML/sub-047029651.html' with directory '/OUTPUTS/BIDS/sub-047029651/figures'
ERROR:missing required output:sourcedata
JOB_FAILED
DONE!

[baxpr]

No files in the PR?

[duettwe]

Oh, yeah, this is the one I pulled into main on accident. I've updated it with some 'changes'.

[baxpr]

Needs to look like https://github.com/VUIIS/yaml_processors/blob/running_processors/fmriprep-ABIDE_v23.2.1.yaml in that section. Some stuff is missing

[baxpr]

Hmm that doesn't seem quite right either. Do you have a test output from the main command that we can review to see where files are at?

[duettwe]

@baxpr - Test COMPLETED on 047_02965_1.

[duettwe]

Oh, this is the one that wasn't quite right. NEVERMIND.

[duettwe]

Hmm that doesn't seem quite right either. Do you have a test output from the main command that we can review to see where files are at?

No, what do you need exactly? This takes all day to run.

[baxpr]

I double checked and that part is actually fine (thought there were going to be extra files in the HTML output but there aren't).

Do we have existing freesurfer for this? If so then in pre we need

    mkdir /INPUTS/freesurfer &&
    mv /INPUTS/SUBJECT/SUBJECT /INPUTS/freesurfer/sub-{subject} &&

before cd /INPUTS

and in main we need to add --fs-subjects-dir /INPUTS/freesurfer

[baxpr]

This use of {subject} is ok because it happens before fmriprep-prep runs

[duettwe]

Updated with freesurfer changes and the post block to match more of what I think we're needing (similarly to ABIDE processor you mentioned previously). Test running now (job 1711335).

[duettwe]

It didn't like those changes.

mv: cannot stat '/OUTPUTS/BIDS/sourcedata': No such file or directory
ERROR:missing required output:sourcedata
JOB_FAILED
DONE!

Does that post need to be something like this:

    rm -fr /OUTPUTS/sourcedata/freesurfer/fsaverage

instead of

    mv /OUTPUTS/BIDS/sourcedata /OUTPUTS/sourcedata &&
    rm -fr /OUTPUTS/sourcedata/freesurfer/fsaverage

The outputs section should be putting that sourcedata into the /OUTPUTS/sourcedata directory right?

[baxpr]

Ah, those would be there if we had freesurfer running internally. PR updated

[duettwe]

Still getting

2025-02-04 02:52:18,450 [IMPORTANT] fMRIPrep finished successfully!
250204-02:52:18,450 nipype.workflow IMPORTANT:
	 Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
2025-02-04 02:52:18,450 [IMPORTANT] Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
ERROR:missing required output:sourcedata
JOB_FAILED
DONE!

[baxpr]

That's easy, I missed it. New commit

[duettwe]

@baxpr - Test COMPLETED on 047_02965_1.

[baxpr]

Do we have a bug ticket for this?

[duettwe]

https://bug.xnat.vanderbilt.edu/bugzilla/show_bug.cgi?id=3235