Re: [Freesurfer] Errors preprocess

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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

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Emma Boyd

Research Technician II

Laboratory for Computational Neuroimaging

Martinos Center for Biomedical Imaging

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lee, Seonjoo <sl3670@cumc.columbia.edumailto:sl3670@cumc.columbia.edu> Sent: Wednesday, July 11, 2018 8:26 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Errors preprocess

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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