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: > External Email - Use Caution > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
