Dear list,
I would like to rotate my orig.mgz volume into chiasmato-commissural space to assess the length of a freesurfer-obtained hippocampal segmentation along the main axis of the hippocampus. I am doing this to enable use of a slice-counting method.
Now, I know that tkregister2 allows me to both rotate volumes and load aseg files, but I can only rotate the movable volume. I'm not clear on how I would set this up a) to rotate my target image in native / subject space (orig.mgz), so as not to disturb the raw length values; or b) to rotate the aseg segmentation along with it.
Is anyone able to offer any suggestions on how I might be able to use freesurfer to accomplish this task (or whether there is a different approach that would be simpler)?
Thanks in advance for any help.
Cheers, Jordan
_____________________________________ Jordan Poppenk Ph.D. Candidate, Department of Psychology University of Toronto, Canada http://individual.utoronto.ca/poppenk
There is no way to peace; peace is the way. - A.J. Muste
If you do it in tkregister2, you can load the orig.mgz as the target and movable, apply the transformations you want, then save the registration matrix. Then use mri_vol2vol to actually resample the volume (either orig or aseg). When applying it to the aseg, you should make sure to use --interp nearest.
doug
Jordan Poppenk wrote:
Dear list,
I would like to rotate my orig.mgz volume into chiasmato-commissural space to assess the length of a freesurfer-obtained hippocampal segmentation along the main axis of the hippocampus. I am doing this to enable use of a slice-counting method.
Now, I know that tkregister2 allows me to both rotate volumes and load aseg files, but I can only rotate the movable volume. I'm not clear on how I would set this up a) to rotate my target image in native / subject space (orig.mgz), so as not to disturb the raw length values; or b) to rotate the aseg segmentation along with it.
Is anyone able to offer any suggestions on how I might be able to use freesurfer to accomplish this task (or whether there is a different approach that would be simpler)?
Thanks in advance for any help.
Cheers, Jordan
Jordan Poppenk Ph.D. Candidate, Department of Psychology University of Toronto, Canada http://individual.utoronto.ca/poppenk
There is no way to peace; peace is the way.
- A.J. Muste
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the suggestion, Doug. The only remaining issue is that I don't know what to give tkregister2 as an initial registration file, since there is no initial registration to be performed to match orig with orig. What should I do? I tried
tkregister2 --s 2499 --mov orig.mgz --targ orig.mgz
... and it will not launch without a registration. Even if I give it the only .dat file I can find in my subject folder --reg mri/ segment.dat, I can't get it to launch.
Cheers, Jordan
On 9-Dec-09, at 3:27 PM, Douglas N Greve wrote:
If you do it in tkregister2, you can load the orig.mgz as the target and movable, apply the transformations you want, then save the registration matrix. Then use mri_vol2vol to actually resample the volume (either orig or aseg). When applying it to the aseg, you should make sure to use --interp nearest.
doug
Jordan Poppenk wrote:
Dear list,
I would like to rotate my orig.mgz volume into chiasmato- commissural space to assess the length of a freesurfer-obtained hippocampal segmentation along the main axis of the hippocampus. I am doing this to enable use of a slice-counting method.
Now, I know that tkregister2 allows me to both rotate volumes and load aseg files, but I can only rotate the movable volume. I'm not clear on how I would set this up a) to rotate my target image in native / subject space (orig.mgz), so as not to disturb the raw length values; or b) to rotate the aseg segmentation along with it.
Is anyone able to offer any suggestions on how I might be able to use freesurfer to accomplish this task (or whether there is a different approach that would be simpler)?
Thanks in advance for any help.
Cheers, Jordan
Jordan Poppenk Ph.D. Candidate, Department of Psychology University of Toronto, Canada http://individual.utoronto.ca/poppenk
There is no way to peace; peace is the way.
- A.J. Muste
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Just use --regheader
Jordan Poppenk wrote:
Thanks for the suggestion, Doug. The only remaining issue is that I don't know what to give tkregister2 as an initial registration file, since there is no initial registration to be performed to match orig with orig. What should I do? I tried
tkregister2 --s 2499 --mov orig.mgz --targ orig.mgz
... and it will not launch without a registration. Even if I give it the only .dat file I can find in my subject folder --reg mri/segment.dat, I can't get it to launch.
Cheers, Jordan
On 9-Dec-09, at 3:27 PM, Douglas N Greve wrote:
If you do it in tkregister2, you can load the orig.mgz as the target and movable, apply the transformations you want, then save the registration matrix. Then use mri_vol2vol to actually resample the volume (either orig or aseg). When applying it to the aseg, you should make sure to use --interp nearest.
doug
Jordan Poppenk wrote:
Dear list,
I would like to rotate my orig.mgz volume into chiasmato-commissural space to assess the length of a freesurfer-obtained hippocampal segmentation along the main axis of the hippocampus. I am doing this to enable use of a slice-counting method.
Now, I know that tkregister2 allows me to both rotate volumes and load aseg files, but I can only rotate the movable volume. I'm not clear on how I would set this up a) to rotate my target image in native / subject space (orig.mgz), so as not to disturb the raw length values; or b) to rotate the aseg segmentation along with it.
Is anyone able to offer any suggestions on how I might be able to use freesurfer to accomplish this task (or whether there is a different approach that would be simpler)?
Thanks in advance for any help.
Cheers, Jordan
Jordan Poppenk Ph.D. Candidate, Department of Psychology University of Toronto, Canada http://individual.utoronto.ca/poppenk
There is no way to peace; peace is the way.
- A.J. Muste
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Jordan Poppenk