Hi Ernest

Take a look at mri_segstats. I think it should do what you want (and it has an extensive help with examples, thanks to Doug)

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Thursday, January 25, 2024 11:31 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Intensity Representation

External Email - Use Caution Dear Freesurfer Team, I registered a Macromolecular Proton Fraction (MPF) map on T1 image using multimodal registration in FSL and used freesurfer for the parcellation as instructed by one of your colleagues. I want to really confirm that whether the intensity is from the MPF as the T1 just provides the anatomical information and the MPF has the information for the myelination. Upon, a discussion with a colleague. He said that when MPF images are registered on T1 images, the intensity represents the MPF values, not the T1 values. This is because the registration process only transforms the spatial coordinates of the MPF images to match the T1 images, but does not alter the signal intensity or contrast of the MPF images. Therefore, the registered MPF images still reflect the macromolecular proton fraction of the brain tissue. Testing it in fsl, the intensity reflects that of the MPF. And a similar process has been found in a article but in their case they used mri_vol2vol. I want to confirm this since I used your software for the analysis. Thank you for your time.