External Email - Use Caution
This works! Thank you so much for your help.
-Seonjoo
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
On Behalf Of Boyd, Emma
Sent: Wednesday, July 11, 2018 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Errors preprocess
Hi Seonjoo,
What directory are you in when you run preproc-sess? You should run this command from the data/ dir.
Emma
---------
Emma Boyd
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lee, Seonjoo <sl3670@cumc.columbia.edu>
Sent: Wednesday, July 11, 2018 8:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Errors preprocess
External Email - Use Caution
Dear Freesurfer experts,
I tried to run preproc-sess but did not have much luck to make it work.
I converted resting fmri file into .nii, and I created the following directory structure and it’s stored under /data/sub1/rest/001/fMRI.nii:
/data
/data/sub1
/data/sub1/rest
/data/sub1/rest/001/
/data/sub1/rest/001/fMRI.nii
Then I ran
preproc-sess -s sub1 -fsd rest
-surface $FSAVERAGE_DIR/fsaverage lhrh -mni305 -fwhm
5 -per-run
And I kept getting the following error message:
ERROR: cound not find session sub1
To run freesurfer I specified SUBEJCTS_DIR as /data (I don’t think it matters, though…)
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
SUBJECTS_DIR=/data
Any suggestion to make it work?
Thanks.
-Seonjoo