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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fotiadis, Panagiotis
<panagiotis.fotia...@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
External Email - Use Caution
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
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