[Freesurfer] V5/MT label anatomical borders
Dear all, is there an anatomical description for the V5/MT label? (Freesurfer Version 4.0.5) Thank you in advance Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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] micro-parcellation
Hello, I've been through the threads and can't find the answer to this one. Problem: - Subdivide the cortex into 5000++ (ideally10,000) units per hemisphere I've tried using mris_divide_parcellation but unfortunately it got very upset trying to find a unique rgb colour after I had managed to achieve 2700 new labels (also I was not entirely sure how to transfer these annot labels to the annot.mgz but that's a side issue): CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid .. etc., I'm not really bothered about visualising the result per se, I just want each small area_ through _the cortical mantel to be assigned an unique value (like in the annot.2009s.mgz images but with many many more areas) so I can then convert to nifti and run numerous MATLAB scripts across multiple coregistered scans. Is this approach going to work?? Cheers, - Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
Re: [Freesurfer] V5/MT label anatomical borders
Hi Christoph, the V5/MT label we distribute is based on the work of Karl Zilles and Katrin Amunts who defined it histologically. I don't have the reference handy, but it shouldn't be too hard to find. cheers Bruce On Tue, 15 Jun 2010, Carl Schultz wrote: Dear all, is there an anatomical description for the V5/MT label? (Freesurfer Version 4.0.5) Thank you in advance Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
Re: [Freesurfer] micro-parcellation
Hi Chris, hmmm, didn't realize that it broke with that many faces. You could try mris_make_face_parcellation. cheers Bruce On Tue, 15 Jun 2010, Christian Lambert wrote: Hello, I've been through the threads and can't find the answer to this one. Problem: - Subdivide the cortex into 5000++ (ideally10,000) units per hemisphere I've tried using mris_divide_parcellation but unfortunately it got very upset trying to find a unique rgb colour after I had managed to achieve 2700 new labels (also I was not entirely sure how to transfer these annot labels to the annot.mgz but that's a side issue): CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid CTABfindRGBi: rgb was invalid .. etc., I'm not really bothered about visualising the result per se, I just want each small area_ through _the cortical mantel to be assigned an unique value (like in the annot.2009s.mgz images but with many many more areas) so I can then convert to nifti and run numerous MATLAB scripts across multiple coregistered scans. Is this approach going to work?? Cheers, - Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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] Antw: Re: V5/MT label anatomical borders
Hi Bruce, thank you for your fast reply. Is that the work you referred to ? Cytoarchitectonic analysis of the human extrastriate cortex in the region of V5/MT+: a probabilistic, stereotaxic map of area hOc5. Malikovic A, Amunts K, Schleicher A, Mohlberg H, Eickhoff SB, Wilms M, Palomero-Gallagher N, Armstrong E, Zilles K. Cereb Cortex. 2007 Mar;17(3):562-74. Best regards Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena Bruce Fischl fis...@nmr.mgh.harvard.edu 15.06.10 14.56 Uhr Hi Christoph, the V5/MT label we distribute is based on the work of Karl Zilles and Katrin Amunts who defined it histologically. I don't have the reference handy, but it shouldn't be too hard to find. cheers Bruce On Tue, 15 Jun 2010, Carl Schultz wrote: Dear all, is there an anatomical description for the V5/MT label? (Freesurfer Version 4.0.5) Thank you in advance Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Antw: Re: V5/MT label anatomical borders
exactly. Bruce On Tue, 15 Jun 2010, Carl Schultz wrote: Hi Bruce, thank you for your fast reply. Is that the work you referred to ? Cytoarchitectonic analysis of the human extrastriate cortex in the region of V5/MT+: a probabilistic, stereotaxic map of area hOc5. Malikovic A, Amunts K, Schleicher A, Mohlberg H, Eickhoff SB, Wilms M, Palomero-Gallagher N, Armstrong E, Zilles K. Cereb Cortex. 2007 Mar;17(3):562-74. Best regards Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena Bruce Fischl fis...@nmr.mgh.harvard.edu 15.06.10 14.56 Uhr Hi Christoph, the V5/MT label we distribute is based on the work of Karl Zilles and Katrin Amunts who defined it histologically. I don't have the reference handy, but it shouldn't be too hard to find. cheers Bruce On Tue, 15 Jun 2010, Carl Schultz wrote: Dear all, is there an anatomical description for the V5/MT label? (Freesurfer Version 4.0.5) Thank you in advance Christoph Christoph Schultz, MD University of Jena Department of Psychiatry 07743 Jena Germany Dr. C. Schultz Universitätsklinik für Psychiatrie und Psychotherapie Philosophenweg 3 07743 Jena Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
Re: [Freesurfer] R: R: How means all the output file from a segmentation?
Hi Leonardo, You might want to check out 3D slicer: http://www.slicer.org/ It sounds like it might be able to do what you're looking for. Best, Mike On Sun, 13 Jun 2010, Leonardo Chesi wrote: Hi bruce, my goal is to obtain a 3D surface of the hippocampal region for a visual comparison with a manual segmentation made by a neuroradiologist. Today I managed to extract the volume with mri_binarize but I can't transform it in a surface that tkurfer can visualize. For that I try to use mri_vol2surf but I obtain a surface with 0 vertices. Can you help me?? Cheers Leonardo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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] Changing tkmedit settings
Hi Folks, In tkmedit, the keyboard commands to view main and aux volume are 'Ctrl+1' and Ctrl+2'. Is it possible for me to change them to just '1' and '2' respectively ? (like how only 'n' is required for the navigation tool) Thanks Mehul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
Re: [Freesurfer] Changing tkmedit settings
Hi Mehul, I actually use alt-c, which is much more convenient as it toggles between them. cheers Bruce On Tue, 15 Jun 2010, Mehul Sampat wrote: Hi Folks, In tkmedit, the keyboard commands to view main and aux volume are 'Ctrl+1' and Ctrl+2'. Is it possible for me to change them to just '1' and '2' respectively ? (like how only 'n' is required for the navigation tool) Thanks Mehul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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] Local gyrification index error
Hi All, I'm running the lGI script on my subjects, and recently received this error: ... remeasuring lGI value for vertex iV = 64101. It may take a few minutes. WARNING -- Problem for vertex iV = 64101, lGI value is aberrantly high (lGI=59.4571)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/misc/data14/jen/SurfaceStats/BCM/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Linux thalamos 2.6.18-194.3.1.el5 #1 SMP Thu May 13 13:08:30 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jun 14 19:20:30 EDT 2010 I've gone to the offending vertex in tkmedit and tksurfer to try to determine if there was some manual editing that needed to be done, but the area appeared to be fine. Any ideas on what the cause/solution might be? Thanks, Nathan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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] segmentation fix question
Hi all, I have a question about fixing surface segmentation errors while doing an anatomical reconstruction. When I try to fix some white matter surface errors by deleting/adding points to wm.mgz and running recon-all -autorecon-wm, they sometimes get fixed only partially or not at all. I was just wondering if there is any way to predict whether a certain volume fix is going to alter a segmentation, or if the only way to find out is to fix the volume and wait for the results of autorecon2. Thanks! Natalia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
Re: [Freesurfer] segmentation fix question
Hi Natalia, you need to figure out what's causing the error in order to understand whether a given fix is going to help. Sorry, I know that's a bit vague, but it really is a case-by-case thing, although there are only a smallish class of different types of problems (maybe 5 or so) Bruce On Tue, 15 Jun 2010, Natalia Bilenko wrote: Hi all, I have a question about fixing surface segmentation errors while doing an anatomical reconstruction. When I try to fix some white matter surface errors by deleting/adding points to wm.mgz and running recon-all -autorecon-wm, they sometimes get fixed only partially or not at all. I was just wondering if there is any way to predict whether a certain volume fix is going to alter a segmentation, or if the only way to find out is to fix the volume and wait for the results of autorecon2. Thanks! Natalia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
