Tags » Freesurfer

How to use the FSL and Freesurfer mailing lists for success in your PhD

FSL is the FMRIB’s Software Library, one of the most widely used neuroimaging analysis packages in the world, and is developed and maintained by the members of the… 1,301 more words

Extracting a volumetric ROI from an annotation file

In the file format of Freesurfer, an annotation file (.annot) contains label values for each vertex and meta information about the labels (structure name strings, color table RGB values). 653 more words

Creating new annotation using a custom classifier

One can create custom annotation using mris_ca_label with a .gcs file, which can be created by mris_ca_train with multiple manual delineations.

The syntax is:

mris_ca_label ${subj} ${hemi} ${canonsurf} ${classifier} ${annotoutfile}
… 47 more words

Getting cortical ROIs from FreeSurfer

The bare minimum information you need to get cortical ROIs from FreeSurfer 867 more words

Splitting the cortical surface into independent regions

FreeSurfer offers excellent visualisation capabilities with tksurfer and FreeView. However, there are endless other possibilities using various different computer graphics software. In previous posts, it was shown here in the blog how to generate… 401 more words


Displaying vertexwise and facewise brain maps

In a previous post, a method to display FreeSurfer cortical regions in arbitrary colours was presented. Suppose that, instead, you would like to display the results from vertexwise or… 1,064 more words