outline.
Hi Doug,
I think I find out where the problem is. Actually the mri_vol2surf
works nicely (and it's also true that tksurfer with -mni152reg samples
the overlay to the white surface by default instead of to the pial
surface.)
The problem is in freeview + rh.aparc.annot.
If you do the following for the attached rh mgh file, you will see it
correctly displayed:
tksurfer fsaverage rh inflated -overlay rh.pial_surface.mni305.mgh
If you overlay this mgh in freeview with rh.inflated surface, but
without loading rh.aparc.annot, it also displays correctly.
However, once I load the rh.aparc.annot, I see something like attached
png.
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
I don't understand what you mean by a "much smaller brain". Can you
elaborate?
On 10/01/2013 06:10 PM, Yang, Daniel wrote:
Hi Doug,
I understand. But the end product turned out to be a much smaller
brain … so I thought there is something wrong. What should I
do here?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 10/1/13 6:00 PM, "Douglas N Greve"
The way the software is set up, you should use
mni152.register.dat
with
mri_vol2surf to map mni152 volumes to the fsaverage (ie
MNI305)
surfaces
doug
On 10/01/2013 05:49 PM, Yang, Daniel wrote:
Hi Doug,
Just checking again, because I haven't heard from
you. So the
purpose
is to use mri_vol2surf is convert MNI152 to a FreeSurfer
(MNI305) mgh
file. I am not sure about the correct register.dat to
use. The
mni152.register.dat is for MNI305 -> MNI152 though.
I'm assuming that there exists some sort of inverse
mni152.register.dat somewhere?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/27/13 6:44 AM, "Yang, Daniel"
Thanks Doug!
Because it maps from a MNI152 space to the
FreeSurfer average
space, do you know what register.dat I can use?
Is it some sort of inverse mni152.register.dat?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/26/13 12:26 PM, "Douglas N Greve"
They might be sampling to different
surfaces. To make
sure
they show the
same exact thing, try mapping the data to
the surface
with
mri_vol2surf
doug
On 09/25/2013 08:31 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I am trying to visualize fMRI activation
(generated from
fsl) on the
fsaverage inflated surface, using
mni152.register.dat.
It's odd that I find the results to be
slightly
different
between
tksurfer and freeview. However, I made
sure that I am
using the same
threshold...
Judging from fslview, I think the result
with
freeview is
more
accurate -- is it due to tksurfer
loading orig.mgz by
default, and
free view loading something else?
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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--
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MGH-NMR Center
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
Douglas N. Greve, Ph.D.