Re: [Freesurfer] Find the fsaverage voxel that corresponds to a voxel in the raw Nifti file

have you seen this description of coordinate systems? https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

On 2/5/19 11:47 AM, ts+ml@rcmd.org wrote:

     External Email - Use Caution

Dear FreeSurfer experts,

I have a raw nifti file created from a stack of DICOM scanner images, let's say it has dimension (162, 172, 188) along the 3 axes. I have also pre-processed this subject in FreeSurfer and have the resulting volume files (e.g., orig.mgz) available.

My question is: For a given voxel in the raw nifti file, how could I find the voxel (or coordinate) in the fsaverage subject that corresponds to this voxel?

I guess this should be a 2 step process:

• first get and apply the affine matrix that leads from the raw file to the Freesurfer pre-processed version (which is resampled to dimension (256, 256, 256) among other changes)
• then get and apply the matrix that leads from the pre-processed subject to fsaverage

But where exactly can I get these matrices from? I guess the talairach.xfm file and some volume like orig.mgz (using mri_info)?

Best,

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer