Use mri_label2vol, not mri_surf2vol.
doug
Behrang Nosrat Makouei wrote:
Hi again,
I am trying to convert a surface segmentation into a volume
file, here is the command I am using:
mri_surf2vol --surfval (???) --hemi lh --surf orig
--volregidentity c2 --template ../mri/rawavg.mgz --outvol orig.img
now my question is what should go to surface value argument. My
understanding from freesurfer surface files was that they store some
kind of values for each vertex too, so when loading a color table, it
simply assigns a color to the vertex values and labels them. So if
surface files already have the surface values, what is this field
actually refers too?
I hope my question is clear enough.
best
On 9/25/06, Doug Greve <[EMAIL PROTECTED]
> wrote:
Look in
$FREESURFER_HOME/FreeSurferColorLUT.txt
Behrang Nosrat Makouei wrote:
Hi,
thanks for help. That was the segmentation i was looking
for. Now the question is what is the look up table Freesurfer uses to
assign values to different labels? in other words, if I want to segment
the " G_postcentral" (for e.g.) what value should i look
for?
bets
On 9/25/06, Doug Greve <[EMAIL PROTECTED]
> wrote:
Have you looked at the aparc+aseg.mgz? It has cortical and subcortical
labelings. You can convert it to analyze with mri_convert.
Behrang Nosrat Makouei wrote:
Hi,
I actually had the some extra question in addition to
the question Shahab had. So i thought to put the questions in the reply.
My final goal is to have Cortical Regions segmented at
the subjects native coordinate space. And I prefer to have the
segmentation in analyze format.
and also, I was wondering if
1- there is a way of saving Surfaces generated with
FreeSurfer into an analyze image.
2- If we can control how fine the cortical segmentation
be. (the number of regions segmented).
Behrang,
On 9/23/06, Bruce Fischl <[EMAIL PROTECTED]
> wrote:
Hi
Shahab,
the ?h.*.annot files are the cortical labelings. What exactly do you wat
to do with them?
cheers,
Bruce
On Sat, 23 Sep 2006, Shahabuddin Ansari wrote:
> Hi,
>
> I can extract subcorical objects from freesurfer segmentation,
since each object is lableled with normalized intesity value. I was
wondering if I can extract different cortical regions in the same
fashion. I can, though, view the labeled cotical surface in tksurfer.
>
> Thanks
> Shahab
>
>
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--
Behrang Nosrat Makouei,
Engineering Science,
MICA Lab (MIAL), TASC 9400, SFU.
cell: 778-885-5016
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--
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:
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--
Behrang Nosrat Makouei,
Engineering Science,
MICA Lab (MIAL), TASC 9400, SFU.
cell: 778-885-5016
--
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
--
Behrang Nosrat Makouei,
Engineering Science,
MICA Lab (MIAL), TASC 9400, SFU.
cell: 778-885-5016
--
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
|
