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
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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