You are on the right track. First, you need a registration matrix. You can get this with bbregister --mov mtr.nii.gz --reg reg.lta --s subject --t2 The above command assumes that GM is brighter than WM in MTR. If this is not the case, then use --t1 View your registration with tkregisterfv --mov mtr.nii.gz --reg reg.lta Then apply it to sample it on the surface (midway between white and pial) with mri_vol2surf  --mov mtr.nii.gz --reg reg.lta --hemi lh --projfrac 0.5 --o lh.mtr.nii.gz If you want to average along the ribbon, you can use --projfrac-avg 0 1 0.1 instead of --projfrac You can then view it with something like tksurferfv subject lh inflated -aparc -ov lh.mtr.nii.gz You may need to adjust the thresholds. You can project it on different surfaces (eg, white and pial)

On 10/5/2023 5:43 AM, Davide Tabarelli wrote:

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Dea FreeSurfer experts,

I’m writing in order to ask how to map on a surface data from a volumetric MTR image.

I have volumetric Magnetization Transfer Ratio data co-registered to the subject native space of a subject (as produced by recon-all on a T1 acquisition). The subject, for which I have also the T1 and T2 scans, has been already processed with recon-all, then I have the complete folder of the subject, as produced by the recon-all standard pipeline.

I need a surface in the native subject space containing the MTR data, averaged along the surface normals for a certain amount of millimeters. It would also be useful to define the surface as in a certain midway between the pial and the white surfaces.

I tried to understand the mri_vol2surf tool but I’m stuck in understanding the correct way to do this and if this is the correct command to be used.

I would greatly appreciate your help !

Thank you in advance.

Davide

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