Dear Fellow Surfers,
After doing a reconstruction with the 3.0 Freesurfer stable version, I checked the Talairach auto-registration with tkregister2. The registration seemed fair enough. However I noticed a strange thing that has not caught my attention before - maybe this a property of the program and/or was there already earlier, maybe it is new, maybe it is a bug, or perhaps my volume is corrupt. The problem/property is observed within the original (target) volume.
After launching tkregister2, if I click inside the target volume, the red cursor moves to that location and other orientations (coronal/sagittal/horizontal) slices also change accordingly (the sliders move). If I have understood correctly, the idea would be that the cursor shows the crossing in all 3 orientations.
However if I look at the brain structure in the three different orientations where my cursor is, it is clearly different in all three images. For example, if I pick a mid-sagittal view and place the red cursor in the thalamus between AC and PC, and then click the "sagittal" button, the cursor is clearly higher (towards top of the head) in the interhemispheric fissure. If I click the "coronal" button, the cursor is in the frontal lobe between the hemispheres (ie much more anterior than the other views).
Is this the way the program is supposed to work, or is this a bug, or is my volume plain corrupted?
*** Here are the specifics: ***
on machine ai
source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT avml07
cd /space/cognito/5/users/raij/subjects_mri
tkregister2 --mgz --s avml07 --fstal
... and there you go, click away...
Thanks for your advice in advance,
Tommi
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
raij@nmr.mgh.harvard.edu
No, that's an annoying little bug that's been there a while. It gets it close, but it is not exact. I've tried to track it down a couple of times. But tkregister2 is a brittle piece of code based on something that Anders wrote about 10 years ago, and it's just very hard to figure out what's going on under the hood. I'll look again ...
doug
On Fri, 7 Apr 2006 raij@nmr.mgh.harvard.edu wrote:
Dear Fellow Surfers,
After doing a reconstruction with the 3.0 Freesurfer stable version, I checked the Talairach auto-registration with tkregister2. The registration seemed fair enough. However I noticed a strange thing that has not caught my attention before - maybe this a property of the program and/or was there already earlier, maybe it is new, maybe it is a bug, or perhaps my volume is corrupt. The problem/property is observed within the original (target) volume.
After launching tkregister2, if I click inside the target volume, the red cursor moves to that location and other orientations (coronal/sagittal/horizontal) slices also change accordingly (the sliders move). If I have understood correctly, the idea would be that the cursor shows the crossing in all 3 orientations.
However if I look at the brain structure in the three different orientations where my cursor is, it is clearly different in all three images. For example, if I pick a mid-sagittal view and place the red cursor in the thalamus between AC and PC, and then click the "sagittal" button, the cursor is clearly higher (towards top of the head) in the interhemispheric fissure. If I click the "coronal" button, the cursor is in the frontal lobe between the hemispheres (ie much more anterior than the other views).
Is this the way the program is supposed to work, or is this a bug, or is my volume plain corrupted?
*** Here are the specifics: ***
on machine ai
source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT avml07
cd /space/cognito/5/users/raij/subjects_mri
tkregister2 --mgz --s avml07 --fstal
... and there you go, click away...
Thanks for your advice in advance,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
raij@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
raij＠nmr.mgh.harvard.edu