External Email - Use Caution
This works! Thank you so much for your help.
-Seonjoo
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Lee, Seonjoo
mailto:sl3...@cumc.columbia.edu>>
Sent: Wednesday, July 11, 2018 8:26 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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
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