I'm not sure what is going wrong with it, but you can do this yourself with

mri_binarize --i aparc+aseg.mgz --match 7  --o bin7.mgz

Then do the same with 8, 46, 47

On 5/17/2021 6:39 PM, A.R. Sekar wrote:

External Email - Use Caution

External Email - Use Caution

Hello experts,

I am doing cerebellar segmentation from one of my previous posts using the command:

isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7,8,46,47

Following the command I am getting an expression syntax error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7,8,46,47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:  7,8,46,47

@: Expression Syntax.

It would be great if you can help me solve this. Thanks!

Akila

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1vNaTYnGTEQZAcbG9_VTLwurdZ_OqoRTQ7WmDDplBcHxdzV...