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Tutorial: Running recon-all on a T1 .nii File

Basic Terms for FS https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_01_BasicTerms.html

Video for recon- all https://www.youtube.com/watch?v=gkjvKMjH7iM

Step 1: Install FreeSurfer

Ensure FreeSurfer is installed on your system. You can download and install it from the FreeSurfer website. Follow the installation instructions specific to your operating system.

Tutorial for install https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=AttachFile&do=get&target=installFS_demo.mp4

Step 2: Set Up FreeSurfer Environment

Set up the FreeSurfer environment variables by adding the following lines to your .bashrc or .bash_profile file:

export FREESURFER_HOME=/Applications/freesurfer/7.4.1
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Step 2a: Reload shell configuration

source ~/.bashrc

Step 3: Set the subjects directory

Example of a local directory here:

export SUBJECTS_DIR=/Users/derekrosenzweig/PycharmProjects/electrodes/freesurfer_subjects

Step 3a: Verify that 'SUBJECTS_DIR' is set correctly

Navigate to the directory where you want the FreeSurfer outputs to be saved:

echo $SUBJECTS_DIR

Step 4: Run recon-all

Run the recon-all command with the full path to the T1 .nii file:

recon-all -s sub-10 -i /Users/derekrosenzweig/PycharmProjects/electrodes/freesurfer_subjects/sub-10_ses-01_T1.nii -all

Alternatively, can run recon-all in parallel through homebrew https://www.youtube.com/watch?v=XHN2tm3tNaw

Consider this as an option depending on the size of your dataset

Step 5: Verify the Output

After recon-all completes (expect this to take several hours), verify the output by checking on an individual subject's directory in your FreeSurfer subjects directory.

ls $SUBJECTS_DIR/sub-09

Within the folder, you should see several subdirectories and files, including mri, surf, stats, etc.

Step 6: Visualize the Results

You can visualize the results using FreeSurfer's visualization tools.

Example 1: View the brain surface reconstruction

freeview -v $SUBJECTS_DIR/sub-08/mri/brain.mgz \
         -f $SUBJECTS_DIR/sub-08/surf/lh.white:edgecolor=blue \
         -f $SUBJECTS_DIR/sub-08/surf/rh.white:edgecolor=red

Example 2: Viewing subcortical structures

freeview -v $SUBJECTS_DIR/sub-08/mri/brain.mgz \
         -v $SUBJECTS_DIR/sub-08/mri/aseg.mgz:colormap=lut

Example 3: Viewing White Matter and Pial Surfaces

freeview -v $SUBJECTS_DIR/sub-08/mri/brain.mgz \
         -f $SUBJECTS_DIR/sub-08/surf/lh.white:edgecolor=blue \
         -f $SUBJECTS_DIR/sub-08/surf/rh.white:edgecolor=blue \
         -f $SUBJECTS_DIR/sub-08/surf/lh.pial:edgecolor=red \
         -f $SUBJECTS_DIR/sub-08/surf/rh.pial:edgecolor=red
freeview -v $SUBJECTS_DIR/sub-08/mri/brain.mgz \
         -f $SUBJECTS_DIR/sub-08/surf/lh.thickness:colormap=heat \
         -f $SUBJECTS_DIR/sub-08/surf/rh.thickness:colormap=heat