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 greve@nmr.mgh.harvard.eduwrote:

...

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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