Hi Freesurfer experts,

I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder.

I used the command mri_label2vol,

mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity

The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture).

Then, I used another methods as follows.

Firstly, I converted the annotation file into some label files using mri_annotation2label command;

Secondly, I created ROIs using these labels by mri_vol2roi.

However, the masks also couldn't cover the gray matter.

Could anyone help me creat good masks?

Thanks a lot!

Zhiwei