It works! Thanks, Doug.

At 2014-11-25 01:19:13, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:
>
>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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>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>greve@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
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