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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
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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 CautionHi 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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