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Missing files (?) and error when using sMRIPrep +fMRIPrep #3358
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As to issue 1, it was not a specific goal of mine to copy precomputed files that did not need modification. It's not obvious that that is generally desirable, as it would make unnecessary copies. For the curv problem, is this reliably reproducible? I can try to look into it. (Note, I'll have very little time to work on this for at least two weeks.) |
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In general, fMRIPrep should do nothing on the structural side that sMRIPrep doesn't do, so it should be safe to copy from sMRIPrep to fMRIPrep. The most likely cause for making new copies of some things and not others is that something is wrong in our logic to not recompute them. |
What happened?
I'm using
smriprep 0.16.1
coupled withfmriprep 24.0.1
. I was attempting to break the workflow down into steps for greater control on when things were ready. My data are multi-session (pre-treatment/post-treatment) with a 3 month(ish) interval. I have T1w and T2w images as well as resting-state BOLD. I ran sMRIPrep first without any obvious errors:Everything appears to be present and runs without error. In the next step, I'm just running the anatomical stage of fMRIPrep and using
--derivatives smriprep=$SMRIPREP
. I know I could do everything all at once, but I have need to apply some filtering for specific subjects on specific sessions because of missing fieldmaps, so I'm doing things piecemeal. When I do this, I run into two issues:There's no native space preprocessed T1w image in the fmriprep/sub-xxx/anat folder, only the T2w image. It's present in the sMRIPrep output.
I get an error (crash logs below).
What command did you use?
What version of fMRIPrep are you running?
24.0.1
How are you running fMRIPrep?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
Anatomical derivatives
Please copy and paste any relevant log output.
Additional information / screenshots
No response
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