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Awesome, thank you Paul!

Best, Panos

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wighton, Paul PWIGHTON@mgh.harvard.edu Date: Wednesday, September 21, 2022 at 5:24 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Voxel to mm coordinates Hi Panos,

Yes that is correct. Taking a voxel value and multiplying it by the vox2ras matrix will give you a coordinate in the "patient coordinate system" which is in mm. RAS denotes that the directions (R)ight, (A)nterior and (S)uperior are positive.

-Paul ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fotiadis, Panagiotis Panagiotis.Fotiadis@pennmedicine.upenn.edu Sent: Wednesday, September 21, 2022 5:07 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Voxel to mm coordinates

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Hello,

I was wondering what the best way would be to extract the coordinates of each voxel in my nifti volume in mm. I have used MRIread to load the nifti volume into Matlab (=mri) and wanted to essentially create a new variable that takes each (voxel) entry in mri.vol and exports its three coordinates in mm. Would I just need to multiply the mri.vox2ras 4x4 matrix to each voxel’s [X Y Z 1]’ (where X,Y,Z are the voxel’s coordinates in mri.vol) or are there different steps involved?

Thank you in advance for your time and help!

Best,

Panos