Re: [Freesurfer] Cortical depth at each cortical voxel

Of course! Please let me know if you have any questions about the toolbox.

Best, Iman

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fotiadis, Panagiotis Sent: Thursday, April 21, 2022 12:32 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical depth at each cortical voxel

Hi Iman,

That is extremely helpful, thank you very much (also the paper is a great read)!

Best, Panos

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Aganj, Iman <IAGANJ@mgh.harvard.edumailto:IAGANJ@mgh.harvard.edu> Date: Thursday, April 21, 2022 at 12:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Cortical depth at each cortical voxel Hi Panos,

You can do such a volumetric analysis using this toolbox:

Code: https://www.nitrc.org/projects/thickness Paper: https://onlinelibrary.wiley.com/doi/epdf/10.1002/hbm.20740

You can apply the MLI_thickness function to the gray matter (soft or binary) mask, which returns the layer thickness at each voxel (Thickness) and the distance of each voxel to the center of the layer (SkeletonDistance). Cortical depth would then be SkeletonDistance at the given voxel subtracted from half of Thickness (at the voxel, or preferably on the skeleton for better accuracy). A tutorial is included in the EXAMPLE file.

Best, Iman

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fotiadis, Panagiotis Sent: Thursday, April 21, 2022 11:48 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cortical depth at each cortical voxel

Hi FS experts,

I was wondering whether there was a way to assign each cortical voxel within the T1w (volumetric) scan an index corresponding to its "cortical depth." I have essentially taken the cortical ribbon .mgz file, assigned each cortical voxel a voxel ID, and wanted to associate each ID with its corresponding cortical depth. I would normally use the *h.sulc files but I didn't think this would properly translate here since it's a volumetric analysis.

Thank you in advance for your time and help!

Best Panos

-- Panagiotis Fotiadis Ph.D. Candidate | Neuroscience Graduate Group Perelman School of Medicine, University of Pennsylvania