Cortical Thickness

Page describing how we analyze cortical thickness with freesurfer

Create a T1 weighted nifti image for the subject

Step 1: In a terminal, convert the PAR/REC files to nifti images. You may not need to do this if you have already gone through the Anatomy Pipeline

cd /home/projects/MRI/[subid]
parrec2nii -c -b *.PAR

Step 2: In MATLAB compute the root mean squared (RMS) image. Once again this might have already been done in the Anatomy Pipeline so you can re-use that RMS image

T1path = 'Path to t1 weighted image';
T1path = mri_rms(T1path); % Root mean squared image

Freesurfer Segmentation

Freesurfer is a useful tool for segmenting a T1-weighted image and building a cortical mesh. To segment the subject's T1-weighted image using freesurfer from the command line type:

recon-all -i /home/projects/anatomy/[subid]/t1_acpc_.nii.gz -subjid [subid] -all