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Dear FreeSurfer experts,
I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins. I am attaching two images to show what I mean.
I would really appreciate some clarification. I am using FreeSurfer 7.1.1
Thanks in advance. José
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_____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1UyleYcIW9IpIEav-uaSJpfZckYD_6rdaRbxs9DgAhomEceC... Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________
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The subcortical GM structures are obtained from the whole brain segmentation (Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the label of the closest point on cortex (Salat, Neuroimage, 2009)
On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins. I am attaching two images to show what I mean.
I would really appreciate some clarification. I am using FreeSurfer 7.1.1
Thanks in advance. José
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* www.uke.de http://secure-web.cisco.com/1TNVlubeEY5RNf4oFHEY5w6gheVEoD4jo9r88zJkPdQ2aOlEQFLWA3ibkhLFQcnM5_K8aBICfUSAq-8vUUHSj-xx2Vssd8w4kXgyf1amgqCTReB780TWu7lTvgcJntfpA-NotaYQz5TDAwpgmUIokpu_mXWyeM1jlwQ5Mt4RYFFQLFUb_dEmXzRqtkPJp7ZaRkGuLZBW01AVPtbv2ULmyM2a6i7CmNrErvQm2kSdAYSiBlMnh2el8dO3zsqImHAkYAjLWT5S4-kKynzWM1352EQ/http%3A%2F%2Fwww.uke.de%2F Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hey, Douglas. Thanks for the answer and the references.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Tuesday, February 2, 2021 5:57:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] White matter parcellation
The subcortical GM structures are obtained from the whole brain segmentation (Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the label of the closest point on cortex (Salat, Neuroimage, 2009)
On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I need help trying to understand how the white matter gets parcellated. I have a clinical dataset, which means that the resolution is not as research images, but it ran without a problem. I would like to measure the volume of the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer decides where a structure ends and the other one begins. I am attaching two images to show what I mean.
I would really appreciate some clarification. I am using FreeSurfer 7.1.1
Thanks in advance. José
________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1YDQZYR7S2qJ4SG_NP8gFjH9ioGs9qVAJxK-GZmNW_gbT-5Q...http://secure-web.cisco.com/1TNVlubeEY5RNf4oFHEY5w6gheVEoD4jo9r88zJkPdQ2aOlEQFLWA3ibkhLFQcnM5_K8aBICfUSAq-8vUUHSj-xx2Vssd8w4kXgyf1amgqCTReB780TWu7lTvgcJntfpA-NotaYQz5TDAwpgmUIokpu_mXWyeM1jlwQ5Mt4RYFFQLFUb_dEmXzRqtkPJp7ZaRkGuLZBW01AVPtbv2ULmyM2a6i7CmNrErvQm2kSdAYSiBlMnh2el8dO3zsqImHAkYAjLWT5S4-kKynzWM1352EQ/http%3A%2F%2Fwww.uke.de%2F Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1zRhx4neXfxE6wjV2715n3qDQ0xa_CZIon5Iy-aK56jikSZ...
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_____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | http://secure-web.cisco.com/1YDQZYR7S2qJ4SG_NP8gFjH9ioGs9qVAJxK-GZmNW_gbT-5Q... Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel _____________________________________________________________________
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Graterol Pérez, José Alberto