no, you should be able to overlay it on and surface configuration or
patch from that hemisphere.
Bruce
On Tue, 30 May 2006, adam walczak wrote:
Thanks...that worked. I am also trying to create a flattened image to overlay
my ROI data on. Will I need to make a new overlay with the flattened image as
the surface template?
Thanks.
Adam
Doug Greve <[EMAIL PROTECTED]> wrote:
You can do it with tksurfer, as in:
tksurfer subject lh inflated -overlay youroverlay.mgh -overlay-reg register.dat
douyg
adam walczak wrote: Thanks Doug...I was also wondering if it were possible to
load our own overlays on the surface (eg. pial surface)?
Would this be done using tksurfer or would some other program/command be needed?
Thanks.
Adam
Doug Greve <[EMAIL PROTECTED]> wrote:
I think I see what you mean. But the answer is no, FreeSurfer will always
resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just
need to make a registration matrix first. Do this:
tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
It is assumed that rawavg.mgz is in the native space (same
This will bring up a window with a control panel. Hit the Compare button. The
two images should be identical. Look at a few slices/orientations to assure
this. Hit the Save Reg button -- this creates register.dat
Then run mri_vol2vol. I've recently modified it and you might not have the most
recent version, so I've copied it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
specify your roi volume as the --mov and use nearest neighbor interp
doug
adam walczak wrote:
Doug,
I think that you answered my question. We wanted to
overlay some ROI files onto the freesurfer created
surfaces, but the ROIs were made before we ran the
images through freesurfer. So we wanted to make sure
that we could keep the surfaces in the same space as
the ROIs we
created...is that an answer to your
question?
Adam
--- Doug Greve <[EMAIL PROTECTED]> wrote:
What do you mean by "native space"? The
reconstruction is not done in
tal space.
doug
adam walczak wrote:
Hello,
I want to make cortical surface images that we
will overlay with our
own masks. But we want to do this in native
space. So, I was
wondering if it is possible to go thorugh the
reconstruction process
to make the surfaces without ever using the
talairach transform and
keeping everything in its native space.
Thank you,
Adam
adam
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