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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Douglas N. Greve, Ph.D.
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