[Freesurfer] White matter

Hi FreeSurfer experts, I know that FreeSurfer genrates WM information (area/volume) for smaller cortical regions (e.g, superiortemporal, supramarginal) along with the GM information. But, I was wondering is there a way to generate larger WM structures (e.g., temporal lobe or parietal lobe) usi

Re: [Freesurfer] Interpreting Covariate Paired Analysis Results

External Email - Use Caution Hello all - reposting this to see if anyone can help - thanks! We are using a paired analysis approach to study cortical thickness in a dataset with 2 timepoints (called pre-protocol and post-protocol). Regarding the mean cluster summary (contrast: [1

Re: [Freesurfer] InfantFS - resampling asset to native space

Hi Fateme, Infant Freesurfer takes a single input image so there is no rawavg file created at the beginning of the pipeline. You should be able to replace rawavg in your command with the original image that you used as an input. Lilla From: freesurfer-bou

Re: [Freesurfer] Tracula error

Hi Anastasia, I did add the ANTs to my path, but am still getting that same error. I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the .csh file which has all the TRACULA configuration info, and also to the bash script that I’m running the trac-all from: export ANTSPATH