With your assurance, I found my problem; the partial brain lines up
fine the with full brain using both tkmedit and tksurfer for the
individual when using the anat2exf.dat conversion matrix. I was
expecting a more "hard-cut" at the edge of the partial brain as
viewed with tksurfer. As an aside, my mris_preproc version is 1.18.2.1.
This actually brings me to the next question regarding partial brain
statistical images: when I perform a group analysis on partial brain
statistical images, should the entire average surface-based brain
contain statistics (sig.mgz)? Depending on the subject, the extent
of brain acquired is different, but does the GLM (using mri_glmfit)
calculate the statistics even where only a subset of subjects have
data? When FSL analyzes such data, it performs the GLM on a mask
that corresponds only to the areas that overlap in all the subjects.
Is there an equivalent mask that can be generated in Freesurfer to
mask out the statistics that are based on a subset of subjects?
I have used mris_preproc to generate cope images (contrast of
parameter estimates) for each subject in average space (which appear
to be correct). I've run mri_concat to "compile" the subjects'
results together, run mri_glmfit, and have resulting statistics that
encompass the entire surface of the average.
Thanks,
Eric
On Nov 22, 2006, at 7:03 PM, Doug Greve wrote:
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
[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
Any information, including protected health information (PHI),
transmitted
in this email is intended only for the person or entity to which
it is
addressed and may contain information that is privileged,
confidential and or
exempt from disclosure under applicable Federal or State law.
Any review,
retransmission, dissemination or other use of or taking of any
action in
reliance upon, protected health information (PHI) by persons or
entities other
than the intended recipient is prohibited. If you received this
email in error,
please contact the sender and delete the material from any
computer.
_______________________________________________
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD
Research Fellow
P.A.I.N. Group
Brain Imaging Center
McLean Hospital
115 Mill Street
Belmont, MA 02478
Phone: 617-855-2475
Fax: 617-855-3772
Any information, including protected health information (PHI),
transmitted
in this email is intended only for the person or entity to which
it is
addressed and may contain information that is privileged,
confidential and or
exempt from disclosure under applicable Federal or State law. Any
review,
retransmission, dissemination or other use of or taking of any
action in
reliance upon, protected health information (PHI) by persons or
entities other
than the intended recipient is prohibited. If you received this
email in error,
please contact the sender and delete the material from any computer.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Eric Moulton PhD
Research Fellow
P.A.I.N. Group
Brain Imaging Center
McLean Hospital
115 Mill Street
Belmont, MA 02478
Phone: 617-855-2475
Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted
in this email is intended only for the person or entity to which it is
addressed and may contain information that is privileged, confidential and or
exempt from disclosure under applicable Federal or State law. Any review,
retransmission, dissemination or other use of or taking of any action in
reliance upon, protected health information (PHI) by persons or entities other
than the intended recipient is prohibited. If you received this email in error,
please contact the sender and delete the material from any computer.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
