Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the aparc annot. You can look in the recon-all.log file for the command line (just make sure to change the output file name too so that you don't overwrite aparc+aseg.mgz)
doug
On 11/24/2014 07:54 AM, wangzhiwei3233 wrote:
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
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