Mapping to the subject's own surface looks promising, but I'm
ultimately not seeing what I think should be correct. Let me give
you some examples of how I've reached this observation. Note that
anat2exf.register.dat is the same for all the command lines listed
below.
Statistical image overlaid on the subject's orig.mgz brain.
tkmedit SUBJ1 orig.mgz lh.white -overlay zstat1.nii.gz -overlay-reg
anat2exf.register.dat
OK - This looks as expected...partial brain statistical map overlying
the full brain in the correct area.
Statistical image overlaid on a "group average" surface-based full brain
tksurfer average lh inflated -overlay zstat1.nii.gz -overlay-reg
anat2exf.register.dat
OK - This seems to match well with the image displayed using tkmedit.
Statistical image overlaid on the subject's surface-based full brain
tksurfer SUBJ1 lh inflated -overlay zstat1.nii.gz -overlay-reg
anat2exf.register.dat
Not OK - Statistical values are spread across the entire full brain.
After I run "mris_preproc --out lh-zstat1.mgz --target average --hemi
lh --mean --iv zstat1.nii.gz anat2exf.register.dat", the output looks
incorrect when viewing the result with the following:
tksurfer average lh inflated -overlay lh-zstat1.mgz
The statistics have spread to fill the surface. Including the flag -
overlay-reg anat2exf.register.dat with this tksurfer command line
offers the same incorrect result.
I hope that this will help us to correct this registration issue.
Any catches as to what might be wrong?
Thanks,
Eric
On Nov 21, 2006, at 5:17 PM, Doug Greve wrote:
Yes, it is possible. As long as the registration looks good in
tkmedit/tkregister2, then it should accurately map to the surface,
even a to a different target surface. What are you using to view
the surface? One thing you should check though is whether it
mapping as expected to the subject's own surface. You can do this with
tksurfer subjname lh inflated -overlay zstat1.nii.gz -overlay-reg
register.dat
doug
[EMAIL PROTECTED] wrote:
Can a partial brain statistical image volume be accurately
registered to a
whole brain surface-based map? When I try to convert a partial brain
statistical file (zstat1.nii.gz, created using FSL) into an
overlay for a
surface-based full brain (created using FreeSurfer), the result is a
statistical overlay that spreads across the entire surface of the
brain. My command line looks like this:
mris_preproc --out lh-zstat1.mgz –target SUBJ1 --hemi lh --mean --iv
zstat1.nii.gz
../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat
My register.dat transformation matrices work fine when I use
tkmedit to
view the cope1.nii.gz image as an overlay of the orig.mgz file
(partial
brain zstats where I would expect them on the image of the full
brain). Does mris_preproc adher strictly to the register.dat
parameters, or is it
possibly over-ridden by the –target surface?
Thanks,
Eric
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Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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In order to help us help you, please follow the steps in:
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Eric Moulton PhD
Research Fellow
P.A.I.N. Group
Brain Imaging Center
McLean Hospital
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please contact the sender and delete the material from any computer.
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