Hi, I've been trying to understand the FScoordinates powerpoint and I would like to ask a few questions (these questions might simply be about mri_convert, depending on where my confusion is...).
1) I think the orig.mgz volume is in the CRS space. Now, looking at slide 8 in the powerpoint, if I want to go from a point in orig.mgz (CRS) to the corresponding point in MNI305 (CRS), I would have to do: inv(Nb)*X*Na*my_point. However, to get the whole volume from orig.mgz to MNI305, the following command does the job:
mri_convert orig.mgz --apply_transform transforms/talariach.xfm -oc 0 0 0 orig.talairach.mgz.
Does this step automatically include the Na and inv(Nb) operations? Or am I wrong about the starting spaces for orig.mgz and MNI305?
2) I get the same result as above for the talairach transform if I use:
mri_convert --apply_transform transforms/talariach.xfm --devolvexfm subjectid -ic 0 0 0 orig talairach.
I see now what devolvexfm is, but which space in the flowchart on slide 8 is it operating on? -ic and -oc seem to be important because I don't get the same results if I use -ic for the first command and -oc for the second command, but I don't find any documentation on what exactly these options do.
Thanks, Leila