Dear Freesurfer experts,
I use freesurfer and when I finish recon-all autorecon1, I would like to transform Brainmask.mgz image back to origin coordination. How to do it ?
Thank replay
Kl chen
if your orig volume is in orig/001.mgz, then you can do:
mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz
cheers, Bruce
On Thu, 31 Aug 2006, tulu wrote:
Dear Freesurfer experts,
I use freesurfer and when I finish recon-all autorecon1, I would like to transform Brainmask.mgz image back to origin coordination. How to do it ?
Thank replay
Kl chen
Hi Bruce,
(aim: transform fs format back to original file format) when I run the commands you suggested: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz the backtransformed image is in the original coordinate boundaries, but it is not a the same position as the original data (see attached example).
Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if your orig volume is in orig/001.mgz, then you can do:
mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz
cheers, Bruce
On Thu, 31 Aug 2006, tulu wrote:
__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Did you have more than 1 run? Try using the rawavg.mgz instead of the 001.mgz if you did.
Bruce On Fri, 1 Sep 2006, Frederick Klauschen wrote:
Hi Bruce,
(aim: transform fs format back to original file format) when I run the commands you suggested: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz the backtransformed image is in the original coordinate boundaries, but it is not a the same position as the original data (see attached example).
Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if your orig volume is in orig/001.mgz, then you can do:
mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz
cheers, Bruce
On Thu, 31 Aug 2006, tulu wrote:
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
p.s. how are you visualizing it? This works fine for me:
mri_convert -rl rawavg.mgz brainmask.mgz brainmask_xformed.mgz tkmedit -f rawavg.mgz -aux brainmask_xformed.mgz
then use alt-c to switch back and forth
Bruce
On Fri, 1 Sep 2006, Frederick Klauschen wrote:
Hi Bruce,
(aim: transform fs format back to original file format) when I run the commands you suggested: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz the backtransformed image is in the original coordinate boundaries, but it is not a the same position as the original data (see attached example).
Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
if your orig volume is in orig/001.mgz, then you can do:
mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz
cheers, Bruce
On Thu, 31 Aug 2006, tulu wrote:
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Hi Bruce,
visualizing with tkmedit works fine for me as well, but when I am loading the backtransformed file brainmask_xformed.mgz with Matlab or plain C I still get the shifted image. Doing the same with the original (pre-FS) image works fine (no coordinate shift).
Thanks, Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. how are you visualizing it? This works fine for me:
mri_convert -rl rawavg.mgz brainmask.mgz brainmask_xformed.mgz tkmedit -f rawavg.mgz -aux brainmask_xformed.mgz
then use alt-c to switch back and forth
Bruce
On Fri, 1 Sep 2006, Frederick Klauschen wrote:
Hi Bruce,
(aim: transform fs format back to original file format) when I run the commands you suggested: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz the backtransformed image is in the original coordinate boundaries, but it is not a the same position as the original data (see attached
example).
Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
if your orig volume is in orig/001.mgz, then you
can
do:
mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz
cheers, Bruce
On Thu, 31 Aug 2006, tulu wrote:
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
hmm, that should put them into the same voxel coords I thought. You can always use the vox2ras given by mri_info to go from one voxel coords to the other.
Bruce On Sat, 2 Sep 2006, Frederick Klauschen wrote:
Hi Bruce,
visualizing with tkmedit works fine for me as well, but when I am loading the backtransformed file brainmask_xformed.mgz with Matlab or plain C I still get the shifted image. Doing the same with the original (pre-FS) image works fine (no coordinate shift).
Thanks, Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. how are you visualizing it? This works fine for me:
mri_convert -rl rawavg.mgz brainmask.mgz brainmask_xformed.mgz tkmedit -f rawavg.mgz -aux brainmask_xformed.mgz
then use alt-c to switch back and forth
Bruce
On Fri, 1 Sep 2006, Frederick Klauschen wrote:
Hi Bruce,
(aim: transform fs format back to original file format) when I run the commands you suggested: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz the backtransformed image is in the original coordinate boundaries, but it is not a the same position as the original data (see attached
example).
Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
if your orig volume is in orig/001.mgz, then you
can
do:
mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz
cheers, Bruce
On Thu, 31 Aug 2006, tulu wrote:
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
You cannot always rely on tkmedit to show you differences between two volumes if their underlying geometry is the same. eg, if you simply reorient coronals into sagitals and make the appropriate changes to the geometry info, then they will show up identically in tkmedit (as they should).
Try this instead:
tkregister2 --mov brainmask.mgz --targ rawavg.mgz --regheader --reg reg.dat --noedit mri_vol2vol --mov brainmask.mgz --targ rawavg.mgz --o brain-in-rawavg.mgz --reg reg.dat --interp nearest
I might need to give you a new version of mri_vol2vol, let me know
doug
Bruce Fischl wrote:
hmm, that should put them into the same voxel coords I thought. You can always use the vox2ras given by mri_info to go from one voxel coords to the other.
Bruce On Sat, 2 Sep 2006, Frederick Klauschen wrote:
Hi Bruce,
visualizing with tkmedit works fine for me as well, but when I am loading the backtransformed file brainmask_xformed.mgz with Matlab or plain C I still get the shifted image. Doing the same with the original (pre-FS) image works fine (no coordinate shift).
Thanks, Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
p.s. how are you visualizing it? This works fine for me:
mri_convert -rl rawavg.mgz brainmask.mgz brainmask_xformed.mgz tkmedit -f rawavg.mgz -aux brainmask_xformed.mgz
then use alt-c to switch back and forth
Bruce
On Fri, 1 Sep 2006, Frederick Klauschen wrote:
Hi Bruce,
(aim: transform fs format back to original file format) when I run the commands you suggested: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz the backtransformed image is in the original coordinate boundaries, but it is not a the same position as the original data (see attached
example).
Frederick
--- Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
if your orig volume is in orig/001.mgz, then you
can
do:
mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz
cheers, Bruce
On Thu, 31 Aug 2006, tulu wrote:
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam
protection around
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Frederick Klauschen -
tulu