we’re having a “up-and-running” singularity container on an sge-server and can use fmriprep successfully on “normal” subjects with that setup.
Now we’re trying to run a particular patient population with the same set-up and would like to explore the possibility of adding already existing freesurfer recon-folder/-files into this pipeline.
Seems that one way of doing this is to add the ‘finished’ recon-subjects’ folder in the respective derivative location?
Also, the data is unique with big anatomical lesions/abnormalities that causes steps with standard recon (and likely other steps later) to fail. That why we processed the data with a dev version of FreeSurfer in the first place. Is there a way of restricting the dependent workflows within fmri prep to only one hemisphere?