Hi,
I am getting consistent errors with one subject. After running:
mri_convert orig orig/orig.mnc mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc
transforms/talairach.xfm (or,
talairach $subj_id talairach2 $subj_id, does not matter)
I check if it is correct:
view the talairach transform in tkmedit by clicking on the VOLUME button to start tkmedit (or starting it directly on the command line), then doing file->transforms->load transform for main volume, and selecting the talairach.xfm. If it is correct, the transferred brain should be slightly tilted forward, and the inter-hemispheric fissure should be pretty much vertical (with x=0 on the midline).
Unfortunately, I am getting a significant leftward shift (in coronal orientation). Surface reconstruction is problematic. For example, in the left hemisphere it seems that no voxels to the right of the (0 0 0) point were used. Therefore, lh surface is 50% of what it should be, topology is very wrong... Any attempt to fix it with manually defining the cutting planes, or editing the volume, failed..
Could you please suggest how to fix talairach transformation?
thank you,
Serge