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: firstname.lastname@example.org 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> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Lee, Seonjoo <sl3...@cumc.columbia.edu<mailto:sl3...@cumc.columbia.edu>> Sent: Wednesday, July 11, 2018 8:26 AM To: email@example.com<mailto:firstname.lastname@example.org> 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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