Useful freesurfer commands to perform various actions.
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project.
Personally I started using freesurfer only a few months ago. At the beginning, I found this package very non-intuitive and complicated. They are open source and their support forum is great, however I failed to find a page that addresses to the beginners questions. Here I am sharing the notes I took while learning how to use this package. If you have questions you can ask me via contact page, even if I am not an expert yet, I enjoy challenging questions.
export ´FREESURFER_HOME=/*data address*/freesurfer_v53/freesurfer
export SUBJECTS_DIR=/*data address*/fsAnatomical
I found the screenshot below via google images and reflects how my terminal appeared after setting these paths and since then every time I open a new terminal tab.
cd /*data address*/Retinotopy/SUBJID/mri/orig
mri_convert SUBJID.nii 001.mgz
recon-all -s SUBJID -all
Coregistration between structural and functional data
tkregister2 --mov *functional data* --s SUBJID --regheader --reg SUBJID/stats/register.dat
bbregister --mov *functional data* --bold \ --s SUBJID \ --init-fsl --reg $SUBJECTS_DIR/SUBJID/stats/register.dat
tkregisterfv --mov *functional data* --reg $SUBJECTS_DIR/SUBJID/stats/register.dat --surfs
Overlay functional data on the cortical surface
“tksurfer” function is the one I use the most often, as I recently realized. This function allows you to overlay volume based masks (ROIs, spmT maps, etc) onto inflated subject surface. Yet, once the interface is ready, you are allowed to shift to pial surface view as well.
tksurfer SUBJID lh inflated -overlay /*path to the spmT volume file*/
e.g. /*first level SPM folder path*/spmT_0001.nii
Export labels to volum based ROIs
Labels are the default region of interest output for the freesurfer. Therefore, they are surface based and not compatible to view with SPM, mriCRO(n). As you might be already used to nifti (*.nii) files, they are volume based. The code below is to convert a surface based label to volume based nifti file. For this we use “mri_label2vol” function.
mri_label2vol --label /*data file*/SUBJID/label/lh.V1_exvivo.thresh.label --temp /*functional image to register on the same space*/ --reg /*data file*/SUBJID/stats/register.dat --fillthresh 0 --subject SUBJID --hemi lh --o /*target destination for the new ROI*/lh_SUBJID_V1.nii