Not running FreeSurfer pipeline
naailk opened this issue · 4 comments
naailk commented
When running the the epitome generated scripts the, freesurfer pipeline is not initiated leading to errors. I have checked the freesurfer directory and could not find a directory for the subject.
aigoyal commented
Hi Naail,
While I try to figure this out, can you please move this/create a new 'issue' in our ... cannlab's branch of this pipeline? It is located at: https://github.com/aigoyal/EPItome-xl/tree/cannlab .
Thanks.
- aman
josephdviviano commented
Please post the error from the termjnal
aigoyal commented
Naail,
A couple of things:
- The master script contained the epi-fsrecon command as
epi-fsrecon /srv/MRI/WORKING/KTEST/T1 /srv/MRI/WORKING/KTEST/proclist_150312_172340_testT1.sh
instead of
epi-fsrecon /srv/MRI/WORKING KTEST T1 /srv/MRI/WORKING/KTEST/proclist_150312_172340_testT1.sh
- And, the associated proclist did not contain any instance of
epi-fsrecon
at all.
I just generated a test pipeline and it worked just fine. Can you try to re-run the pipeline for this experiment/subject and see if this happens again?!
josephdviviano commented
I'm going to close this issue as I think it is resolved..