According to this, it was able to read/write ribbon.mgz. Are you still seeing the same errors? And is the ribbon.mgz file viewable in mricron?
What fMRIPrep prints to the screen while it runs.
I’m getting the same error message when I view it in MRIcron.
Would you be able to email me brain.mgz and ribbon.mgz from one of these subjects? You can use this username @ gmail.com.
Sure thing, I already sent you an email with the following files.
Hi,
Here’s an update from my side. So, I managed to run the code using --fs-no-reconall and fMRIPprep completed successfully!
However, do you know of a way that I could run reconall separately? (I was reading some posts on Neurostars and people have used this method and it worked for them but they did not describe how they did so).
I would be grateful if someone (who used this method) could provide details on the script used.
Many thanks,
Rubina
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
You can set $SUBJECTS_DIR to be inside your BIDS derivatives folder (so freesurfer will make outputs there).
Then, using your fmriprep singularity container, you can try something like:
singularity exec -B "/important/drives" /path/to/fmriprep.img recon-all -all -subjid $SUBJECTID -i /path/to/raw/t1.nii