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Nope, but Based on the ctable every region has an ID, something like "632550" but sometimes when I read the lh.aparc.annot using matlab, I read labels values equal to 0, which has no match in the ctable.
I don't understand if these zeros represent an unknown area, or is it a bug?
I assign all vertices, with label values equal to zeros, to the unknown region, however, the unknown region already has a label value in the ctable. That's what I don't understand
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, August 27, 2018 2:36:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Parcellation labels error
was there something other than CC that had 0 number of verts?
b'unknown' contains: 6695 b'insula' contains: 3551 b'temporalpole' contains: 552 b'precuneus' contains: 5189 b'frontalpole' contains: 351 b'transversetemporal' contains: 695 b'supramarginal' contains: 5915 b'superiorfrontal' contains: 9823 b'superiortemporal' contains: 5738 b'parstriangularis' contains: 2286 b'rostralmiddlefrontal' contains: 7656 b'medialorbitofrontal' contains: 2167 b'isthmuscingulate' contains: 1359 b'superiorparietal' contains: 7060 b'lateraloccipital' contains: 7440 b'lateralorbitofrontal' contains: 3510 b'fusiform' contains: 4661 b'posteriorcingulate' contains: 1783 b'inferiorparietal' contains: 6607 b'parahippocampal' contains: 965 b'caudalanteriorcingulate' contains: 779 b'parsopercularis' contains: 2422 b'rostralanteriorcingulate' contains: 853 b'precentral' contains: 6554 b'lingual' contains: 3628 b'postcentral' contains: 6424 b'bankssts' contains: 1613 b'corpuscallosum' contains: 0 b'paracentral' contains: 2045 b'parsorbitalis' contains: 936 b'entorhinal' contains: 458 b'caudalmiddlefrontal' contains: 2994 b'pericalcarine' contains: 1564 b'inferiortemporal' contains: 5501 b'middletemporal' contains: 5220 b'cuneus' contains: 2000
On 08/27/2018 12:09 PM, Ali,Mohamed Tarek Mohamed wrote:
External Email - Use Cautionand what about the 0's showing up in labels?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, August 27, 2018 11:04:01 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Parcellation labels error Neither the aparc nor the aparc.DKTatlas have corpus callosum labeled. It is labled in the aseg.mgz though
On 08/27/2018 10:24 AM, Ali,Mohamed Tarek Mohamed wrote:
External Email - Use CautionHello FreeSurfer Developers,
While I am using [vec,labels,cnames] = read_annotation('lh.aparc.annot'), I am getting values in labels which are not found in cnames.table(:,5). These values are 0. I assigned the values to the unknown area. However, when I looked at the number of vertices per brain regions I found that corpuscallosum has no vertices in the DK atlas.
This is my first week using a neuroimaging software and Freesurfer is my first software to work on, so I just don't know if that's ok or if there is something wrong.
I am attaching the output of a python code I wrote to count the number of vertices per brain region in the left hemisphere of a structural MRI image from our dataset.
Thanks in advance,
*Mohamed T. Ali*
*Ph.D. student, Bioengineering,*
*University of Louisville.*
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