Hi Doug,
In order to compute and apply the inverse of an m3z transform you would need to use the --inv-morph flag instead of the --m3z and reverse your targ and mov inputs. With the current implementation of mri_vol2vol though I do not think that you can specify the order of the transforms (which is important here), so you would need to apply the inverse non-linear trasform first and then the inverse rigid.
Lilla
On Wed, 25 Jan 2017, Douglas Merkitch wrote:
Hello Freesurfer experts, From your wiki page, I understand how to normalize volumes in subject diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov fa-masked.mgz \ --o fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg
However, how would one take take a volume in CVS template space and reverse normalize it back to subject diffusion space? Is this possible? If so, what would that command look like and what other st eps would be necessary to get the required inputs?
Thanks,
Doug
Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch@rush.edu