I created a matlab file called annotval2surfoverlay.m. Does this do what you want?
surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile)
Example: I have three annotations annotnames = strvcat('superiortemporal','insula','postcentral'); with matchine values annotvals = [1.1 2.2 3.7]; I want to create a surface overlay with all the vertices in a given annotation having its corresponding value (ie, all vertices in superior temporal gyrus being a value of 1.1, etc)
Run these commands in matlab annotnames = strvcat('superiortemporal','insula','postcentral'); annotvals = [1.1 2.2 3.7]; annotfile = '~/subjects/fsaverage/label/lh.aparc.annot'; surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile); clear mri mri.vol = surfoverlay; MRIwrite(mri,'vals.mgh');
Run this command from a linux shell: tksurferfv fsaverage lh inflated -aparc -ov vals.mgh -fminmax .01 1
On 5/14/19 10:41 AM, albertotricker wrote:
External Email - Use CautionI hava a data set of 240 patients, 60 Healthy Control, 60 MCI, 60 cMCI and 60 AD, with 429 cortical and subcortical features.
68 of this features are cortical thickness standard desviation features (ie, lh_bankssts_thicknessstd, lh_caudalanteriorcingulate_thicknessstd, … , rh_insula_thicknessstd). I have calculated the average of each of this features for each group (HC, MCI, cMCI, AD) and I want to represent this data over a brain template. For now I am doing this with visbrain, a Python open-source package, but I was wondering if I could do the same with FreeSurfer. I have not found any way to do it in a simple way in the FreeSurfer wiki, but there has to be some way to do it.
Thanks you for the help!