If you can get the voxel sizes and number of rows, cols, and slices, then the vox2ras-tkr is pretty easy to compute. Search our wiki for coordinates. This page will have a power point presentation that includes how to compute it. doug

On 3/21/13 10:02 PM, Eric Larson wrote:

Does anyone have code available for reading the vox2ras-tkr transform from .mgz files? I am working on implementing the transform outlined on the Freesurfer wiki:

MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'

TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info --vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz

I can get vox2ras-tkr (a.k.a., Torig) using mri_info, but it would be better if they were available in the python package nibabel for use in mne-python (for easy conversion from surface to MNI coordinates). nibabel already supports reading the --vox2ras transform, but I need to code the other one in order to avoid a dependecy in our code. Does anyone have code to extract that information? MATLAB, Python, C code, or heck, even pseudocode would help. If not, if anyone has helpful information on the specs on the .mgz specification, maybe it won't be too difficult to code from scratch...

Eric

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