josephdviviano/epitome

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:

  1. 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
  2. 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..