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Copy to local SUBJECTS_DIR

A configuration file is used to define subjects and locations.

The following commands are examples of running the preprocessing steps:

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1) In Linux, check that you have a folder

/usr/local/freesurfer/subjects

If not, create it. This will also need the bert and fsaverage folders copied to it.

2) copy the T1 FreeSurfer subject to this folder. An example of a command (from a terminal in Linux):

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

3) Copy the DTI data to the subjects folder

]$ cp -rv /mnt/hgfs/LinuxShare/

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subjects4FSL/CON302/DTI_b0corr /usr/local/freesurfer/subjects/CON302/

 Make sure the bvals4tracula.txt and bvecs4tracula.txt files are included. If not, create them and copy them individually:

cp /mnt/hgfs/LinuxShare/subjects4FSL/CON302/DTI_b0corr/*4tracula.txt /usr/local/freesurfer/subjects/CON302/DTI_b0corr

Configuration File (dmrirc)

This is a required file which is passed to the TRACULA processing steps. A reasonable place to save this is LinuxShare\tracula.

• Example

• A configuration file is used to define subjects and locations.

  The following commands are examples of running the preprocessing steps:

  Background Color
  tracl-all -c /mnt/hgfs/LinuxShare/tracula/dmrirc -prep

FreeSurfer Preprocessing

Make sure each subject has a successfully completed FreeSurfer preprocessing set of files.

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