Hi Vin,
we don't currently segment any thalamic nuclei, although hope to do so in
the future.
cheers,
Bruce
On Mon, 10 Nov 2008, vin wrote:
*Hi Doug, *
*Greetings!! *
complete thalamus ROI extraction works, but when I tried segmented thalamic
nuclei, than output file doesn't contain anything.
*>mri_binarize --i aseg.mgz --match 8001 --o thalamus_nuclei_fs.nii*
this how output looks like :
input aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output thalamus_nuclei_fs.nii
Binarizing based on matching values
nMatch 1
0 8001
binval 1
binvalnot 0
Found 0 values in range
mri_binarize done
should I choose some other file expect aseg.nii.gz ? to get thalamic nuclie
.
thank you very much !!
vin
*
*
On Tue, Nov 4, 2008 at 4:42 PM, Doug Greve <[EMAIL PROTECTED]>wrote:
They are in aseg.mgz, you can extract them into a nifti file with
mri_binarize --i aseg.mgz --match 251 --o CC_Posterior.nii
251 is the code for CC Posterior (found in
$FREESURFER_HOME/FreeSurferColorLUT.txt)
doug
vin wrote:
hi,
I am trying to export segmented regions as NIFTI, and it works for the
regions like Thalamus whole. But when freesurfer finished autorecon, than
it showed lot of sub regions for example : Thalamic sub regions and also
CC_Posterior, CC_Mid_Posterior, CC_central (CC= Corpus Callosum) and...Mid
anterior and Anterior.
How I can get these sub regions. In which files they are stored, and How I
can extract them as NIFTI format.
any suggestion would be great !!
thank you very much ,
vin
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