Hi Anna

if you have dicoms that are T1-weighted and about 1mm isotropic (less than say 1.3mm in any direction), just give them to recon-all as input and it will essentially do everything in native space (and will take 12-20 hours depending on hardware/anatomy)

cheers Bruce

On Mon, 25 Apr 2016, Anna Harris wrote:

Hi,

I'm writing from UChicago to inquire as to what the easiest way to calculate ventricular volumes is using the segmentation tools. I'm having a hard time navigating your wiki. If there is a command line protocol for this listed, can you please refer me to it? Otherwise I may need help walking through the steps, as I've just recently been trained on SPM. I'm also not sure whether if the MRI images I have collected are already standardized, if I need to re-preprocess them in Freesurfer to be able to use the segmentation tools properly.

Please advise! Many thanks, Anna