Hi,
I'm trying to move a bunch of partial FOV functional images (occipital cortex only with oblique coronal slices) into common space. For each subject, I have a registration file (register.dat) to register functional images to anatomicals, and I'd like to incorporate the talairach.xfm registration so that I have a matrix that registers the functional images to the mni305 volume. I've been using the following, but registrations aren't coming out properly:
mri_matrix_multiply -im register.dat -iim <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat
I'm checking them using tkregister2, but the results don't look great. Is there a better/easier way to do this? Thanks!
Andrew
Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or --talres 1 for 1mm isotropic) option. This will put it into an MNI305 space. So something like
mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o yourvolume.mni305.nii
If you did not create the register.dat with bbregister, I would strongly suggest it. It works really well on the partial volume files. If you do, you should specify your current register.dat as the init registration.
doug
Andrew Dumas wrote:
Hi,
I'm trying to move a bunch of partial FOV functional images (occipital cortex only with oblique coronal slices) into common space. For each subject, I have a registration file (register.dat) to register functional images to anatomicals, and I'd like to incorporate the talairach.xfm registration so that I have a matrix that registers the functional images to the mni305 volume. I've been using the following, but registrations aren't coming out properly:
mri_matrix_multiply -im register.dat -iim <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat
I'm checking them using tkregister2, but the results don't look great. Is there a better/easier way to do this? Thanks!
Andrew
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug! One more question-- How can I invert this registration? I want to move the volumes in the common space back to each original subject space. mri_vol2vol won't accept a --targ when I specify --tal, but I'd like to use --inv.
Andrew
On Tue, 2011-12-20 at 14:58 -0500, Douglas N Greve wrote:
Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or --talres 1 for 1mm isotropic) option. This will put it into an MNI305 space. So something like
mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o yourvolume.mni305.nii
If you did not create the register.dat with bbregister, I would strongly suggest it. It works really well on the partial volume files. If you do, you should specify your current register.dat as the init registration.
doug
Andrew Dumas wrote:
Hi,
I'm trying to move a bunch of partial FOV functional images (occipital cortex only with oblique coronal slices) into common space. For each subject, I have a registration file (register.dat) to register functional images to anatomicals, and I'd like to incorporate the talairach.xfm registration so that I have a matrix that registers the functional images to the mni305 volume. I've been using the following, but registrations aren't coming out properly:
mri_matrix_multiply -im register.dat -iim <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat
I'm checking them using tkregister2, but the results don't look great. Is there a better/easier way to do this? Thanks!
Andrew
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
When you run your original mri_vol2vol command, add --reg-final reg.final.dat. You can then use
mri_vol2vol --reg reg.final.dat --mov yourmovvol.nii --targ yourvolume.mni305.nii --inv --o new.yourmovvol.nii
to map it back to the moveable space doug
Andrew Dumas wrote:
Thanks, Doug! One more question-- How can I invert this registration? I want to move the volumes in the common space back to each original subject space. mri_vol2vol won't accept a --targ when I specify --tal, but I'd like to use --inv.
Andrew
On Tue, 2011-12-20 at 14:58 -0500, Douglas N Greve wrote:
Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or --talres 1 for 1mm isotropic) option. This will put it into an MNI305 space. So something like
mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o yourvolume.mni305.nii
If you did not create the register.dat with bbregister, I would strongly suggest it. It works really well on the partial volume files. If you do, you should specify your current register.dat as the init registration.
doug
Andrew Dumas wrote:
Hi,
I'm trying to move a bunch of partial FOV functional images (occipital cortex only with oblique coronal slices) into common space. For each subject, I have a registration file (register.dat) to register functional images to anatomicals, and I'd like to incorporate the talairach.xfm registration so that I have a matrix that registers the functional images to the mni305 volume. I've been using the following, but registrations aren't coming out properly:
mri_matrix_multiply -im register.dat -iim <subject>/mri/transforms/talairach.xfm -om reg_to_common.dat
I'm checking them using tkregister2, but the results don't look great. Is there a better/easier way to do this? Thanks!
Andrew
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Andrew Dumas -
Douglas N Greve