Page Comparison

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...]$ freeview -v /usr/local/freesurfer/subjects/CON302/dmri/dtifit_FA.nii.gz -tv /usr/local/freesurfer/subjects/CON302/dpath/merged_avg33_mni_bbr.mgz

FreeSurfer Preprocessing

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Saving Outputs

You will want to copy the results back to the LinuxShare. All TRACULA outputs are in the subject "dmri" subfolders:

...]$ cp -rv /usr/local/freesurfer/subjects/CON302/dmri* /mnt/hgfs/LinuxShare/subjects4freesurfer/CON302

 The results will be available to everyone. Viewing paths and measure stats will require adjusting the file location.

DTI Data

Probably easiest to use an outside folder; if DICOM files are available, these will work (at least for Siemens scanners). Otherwise, the format is akin to FSL.

• Note that for Linux, spaces are a problem, so the file names must have spaces removed.

Technical Note: Issues running in a VM*

The scripts rely on symbolic links, which cannot be created on Windows shared folders. Thus, the SUBJECTS_DIR must be local, and under the usual VM setup we use, the files need to be copied locally, and the local SUBJECTS_DIR set.

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