Hmm, there's something fishy here. If the tkmedit command worked, then the 2nd tksurfer cmd (onto SUBJ1) should have worked. The first tksurfer command should NOT have worked as the registration would not be correct for for the average subject. Are you sure you did not reverse these? Which version of mris_preproc are you running? Run with --version to check.
doug
On Wed, 22 Nov 2006, Eric Moulton wrote:
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
emoulton@mclean.harvard.edu 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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