You can use the per-voxel regressor (--pvr) option to mri_glmfit. Search through the mail archives for how to use it

On 10/23/2018 06:34 AM, Damien MARIE wrote:

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Hi Matt,

Many thanks for your prompt reply, you are right.

Any tips on how I could do that?

Should I regress out cortical thickness from my myelin maps at the individual level, save the individual output myelin maps and run analyses on the latter? If yes how?

That’s really important to me otherwise a reviewer could claim the myelin differences we detect might be supported by cortical thickness variations and not myelin…

Thank you and best,

Damien

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Glasser, Matthew https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Glasser%2C+Matthew%22Mon, 22 Oct 2018 12:57:43 -0700 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20181022

Regression would be better than division. Matt.

From: <freesurfer-boun...@nmr.mgh.harvard.edu http://nmr.mgh.harvard.edu/mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Damien MARIE <damien.ma http://damien.ma/...@unige.ch http://unige.ch/mailto:damien.ma...@unige.ch> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, October 22, 2018 at 8:54 AM To: "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Myelinated cortical thickness ratio map

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Dear experts,

I am working with R1 maps that I project on the surface. The goal is to look at intra-cortical myelin.

I detect interesting effects between two groups. Now I would like to compute myelinated cortical thickness ratio maps, in order to control for the effect of cortical thickness variations occurring with gyrification.

Here is a paper where they describe a way to compute those myelinated cortical thickness ratio map with MIPAV and the MPI-CBS toolbox : https://www.ncbi.nlm.nih.gov/pubmed/29321232 « The proportional thickness of the myelinated part of the cortex in relation to its overall thickness (myelinated cortical thickness) was computed with a fuzzy classification technique combining information about radial and tangential fibers. «

1- Is it possible to do the same in FreeSurfer?

2- What about dividing my individual myelin maps by the individual cortical thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do the job in the volume but I don’t know how I could do that in FreeSurfer.

Any comments / other suggestions are welcome.

Thank you and best,

Damien

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