Use either mri_aparc2aseg (v6) or mri_surf2volseg (v7). These are used to create the aparc+aseg.mgz. You can look in the recon-all.log file for an example command line.


On 8/17/2020 5:03 PM, Thomas Alderson wrote:

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Dear Freesurfer experts,


Although this issue was raised in the archive, I could not find an answer.

        
I want to create a 3d volume using an annot file. 

        

        
I run the following command.

        

        
'mri_label2vol --annot $SUBJECTS_DIR/' subj '/label/lh.Schaefer2018_100Parcels_7Networks_order.annot --temp $SUBJECTS_DIR/' subj '/mri/orig.mgz --identity --fillthresh .3 --subject ' subj ' --hemi lh --o $SUBJECTS_DIR/' subj '/schaefer_volume_left.nii.gz --proj frac 0 1 .1'


        
    


        
This produces a 3d volume but the ribbon is not well filled (it's patchy and extends outside the ribbon).

        

        
I tried to use --fill-ribbon but this produces a binary volume of the ribbon without the label information from my annot file.


        

        
How can I convert my annot into a 3d volume that completely fills the ribbon and retains label information? 

        
Thank you.

-Tom.

      

      

      

      
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