External Email - Use Caution
Hello 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.
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 Caution
Hello 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.*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
and 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.*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Caution
and 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 Caution
Hello 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.*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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.*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Ali,Mohamed Tarek Mohamed -
Douglas N. Greve