External Email - Use Caution        

This works! Thank you so much for your help.

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 Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging

 on behalf of Lee, Seonjoo 
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:






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, 

export FREESURFER_HOME=/Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh


Any suggestion to make it work?



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