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That sounds  like a perfect plan! 

I gonna try that immediately! Thanks so much, Doug!
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Wednesday, 22 May 2019 6:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] Checking number of parcels after transformation of an annotation file into a .nii.gz file
 
External Email. Use Caution.

the way that pops to mind is to use matlab
a = MRIread('aparc.250+2mm.nii.gz');

u = unique(a.vol(:));
length(u) will give you the number of unique segmentation number
(including 0)

On 5/22/19 5:54 PM, Winkelbeiner, Stephanie A wrote:
>
>         External Email - Use Caution
>
> Hi Freesurfers,
>
> I'm struggling to find out if the number of parcels during a process
> of transformations from annot -> nii.gz has changed.
>
> I extended the parcels from 500.annot 2mm into the WM with
> mri_aparc2aseg \
> --s s001 \
> --annot 500.aparc \
> --wmparc-dmax 2 \
> --labelwm \
> --hypo-as-wm \
> --o mri/aparc.250+2mm.nii.gz
> and coregistered the resulting file to the DWI image using bbregister
> and mri_vol2vol.
>
> Using afni's probilistic tractography pipeline, I end up with more
> parcels than I thought I had.
>
> Is there a way to check the number of parcels after extension into the
> WM (mri_aparc2aseg)?
>
> I would be extremely grateful for some insight!
> Thanks,
> Stephanie
>
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