Hi Doug,

sorry for my inability to read... fscoordinates.pdf makes it rathe clear that tkrvox2ras actually always is constant and only ever reflects freesurfer LIA to freesurfer RAS, even if the input volume is not in LIA. I had foolishly expected it to always map to freesurfer RAS from the current orientation. Sorry for the confusion....

best Sebastian

Begin forwarded message:

From: Sebastian Moeller sebastian.moeller1@rwth-aachen.de Date: August 29, 2011 17:10:20 PM PDT To: "freesurfer@nmr.mgh.harvard.edu List" freesurfer@nmr.mgh.harvard.edu, Douglas N Greve greve@nmr.mgh.harvard.edu Bcc: Sebastian Moeller sebastian.moeller1@rwth-aachen.de Subject: mri_convert -conform issue

Hi List,

I just noticed that when I use mri_convert -conform (which reslices my RPI volumes to LIA) the tkrvox2vras matrices seem not to change (for both freesurfer centos4 64bit, version 4.5 and version 5.1). I use MRIread to read in the resulting files in matlat and try to compare the volumes there. All the vox2ras are changed by the conformation (as I expect), but the tkrvox2ras of the conformed volume equal the tkrvox2ras matrix from the original volume. I am confused now as the tkrvox2ras and the x_r, x_a, x_s, (as well as the y_* and z_*) vectors are updated and match the vox2ras matrices. Shouldn't tkrvox2ras also be updated? And if not why :) ?

Best Sebastian

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