Cortical Thickness

Page describing how we analyze cortical thickness with freesurfer

Setting up Freesurfer and MATLAB

First make sure that you have the correct lines in your .bashrc file to run freesurfer:

export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh > /dev/null
export SUBJECTS_DIR=/mnt/diskArray/projects/freesurfer

Next make sure that you have the right tool boxes in your matlab search path. This should be done through your startup.m file

addpath(genpath('~/git/yeatmanlab'));

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 /mnt/diskArray/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/MRI/[subjid]/[YYYYMMDD]/[subjid]_WIP_MEMP_VBM_SENSE_13_1_MSE.nii.gz -subjid [subid] -all

We will follow the steps outlined in the Freesurfer Wiki for analyzing cortical thickness. The first steps are described here