Hello, We are looking for a way to reorient the orig.mgz files and the segmentation (aseg.mgz) into a different plane, and we have a couple of questions. We've used tkregister2 to reorient the orig image:
tkregister2 –mov orig.mgz –tar orig.mgz –regheader –reg myregister.dat myregister.dat is created by this command line. We rotate the brain in the tkregister2 gui, then save the registration. Finally, we use the mri_vol2vol command line to rotate the orig and the aseg images. For aseg.mgz: mri_vol2vol --mov aseg.mgz --targ orig.mgz --reg myregister.dat --interp nearest --o rotaseg.mgz For orig.mgz: mri_vol2vol --mov orig.mgz --targ aseg.mgz --reg myregister.dat --o rotorig.mgz This seems to look decent when we load it up in tkmedit, but we have two questions about the use of mri_vol2vol 1) Why does the algorithm need a target (won't run without it), since the transformation info is saved in myregister.dat? Also, how does it manage to work (which it does), given than neither of the targets entered are in the reoriented space? Should we use a different target? What is the role of the target? 2) A previous post specifies that "interp nearest" should be used to rotate the aseg.mgz file. What is the function played by that command? Should we also use it when rotating the orig.mgz file? It works without it, but do we risk distorting the image? Thanks in advance! Tim Al-Khindi
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