[Freesurfer] equivalent of BrainSegVol in Freesurfer V5.0
Hi, BrainSegVol and BrainSegNVoxare removed from the newest version (v5.0) of Freesurfer. I was wondering what is the equivalent variable for BrainSegVol? Thank you, Amir -- Amir M. Tahmasebi, Ph.D. Postdoctoral Research Fellow Rotman Research Institute, University of Toronto, Toronto, Ontario CANADA Tel: (416) 785-2500, ext. 3130 Web: www.cs.queensu.ca/~tahmaseb ___ 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] POSTDOCTORAL POSITION - Neuroimaging and Brain Plasticity
Please see the attached file. If interested, pelase submit your C.V. and relevant reprints, together with a cover letter describing current research interests and future research goals, and also arrange to have three letters of reference sent independently to: Dr. Sylvain Moreno Rotman Research Institute Baycrest 3560 Bathurst Street Toronto, Ontario, M6A 2E1, Canada E-mail: smor...@rotman-baycrest.on.ca Amir M. Tahmasebi, Ph.D. Postdoctoral Research Fellow Rotman Research Institute, University of Toronto, Toronto, Ontario CANADA Tel: (416) 785-2500, ext. 3130 Web: www.cs.queensu.ca/~tahmaseb Postdoc Fellowship - ad.pdf Description: Adobe PDF document ___ 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] extracting sulcal ribbons
Thanks Bruce for your reply. This is actually helpful. Could you please briefly describe how can I generate the skeleton? Thank you, Amir On 1/27/2011 10:33 AM, Bruce Fischl wrote: no, sorry, we don't generate sulcal ribbons, although it wouldn't be too hard to generate a skeleton from the flattened parcellaton cheers Bruce On Wed, 26 Jan 2011, Amir Tahmasebi wrote: Dear experts, I would like to extract certain sulcal ribbons from brain surface and create a probability map for each sulcus type. I was wondering if freesurfer generates sulcal ribbons (or sulci curves on the flatten surface) in the subject space. Thank you, Amir On 1/26/2011 3:13 PM, Michael Harms wrote: Hi Justin, It partly depends on what exactly you want when you say brain volume. Do you want a measure of estimated intracranial volume (intended to be independent of atrophy)? A measure of gray matter + white matter + ventricles? Or only gray matter + white matter? Do you care whether the cerebellum is included or not? cheers, -MH On Wed, 2011-01-26 at 12:52 -0600, Justin Eisenberg wrote: Hi all, What is the best way to calculate total brain volume? It seems that there are multiple ways to do it--mris_volume and mris_wm_volume, add up the structures in the aseg.stats and ?h.aparc.stats files, or using the BrainSegVol or BrainSegVolNotVent from aseg.stats. What do you recommend? Thanks! Justin -- Justin Eisenberg Washington University in St. Louis Arts Sciences | 2013 jeisenb...@wustl.edu jeisenberg...@gmail.com 262.914.4648 ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Amir M. Tahmasebi, Ph.D. postdoctoral researcher Rotman Research Institute, University of Toronto, Toronto, Ontario CANADA Tel: (416) 785-2500, ext. 3130 Web: www.cs.queensu.ca/~tahmaseb ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] extracting sulcal ribbons
Dear experts, I would like to extract certain sulcal ribbons from brain surface and create a probability map for each sulcus type. I was wondering if freesurfer generates sulcal ribbons (or sulci curves on the flatten surface) in the subject space. Thank you, Amir On 1/26/2011 3:13 PM, Michael Harms wrote: Hi Justin, It partly depends on what exactly you want when you say brain volume. Do you want a measure of estimated intracranial volume (intended to be independent of atrophy)? A measure of gray matter + white matter + ventricles? Or only gray matter + white matter? Do you care whether the cerebellum is included or not? cheers, -MH On Wed, 2011-01-26 at 12:52 -0600, Justin Eisenberg wrote: Hi all, What is the best way to calculate total brain volume? It seems that there are multiple ways to do it--mris_volume and mris_wm_volume, add up the structures in the aseg.stats and ?h.aparc.stats files, or using the BrainSegVol or BrainSegVolNotVent from aseg.stats. What do you recommend? Thanks! Justin -- Justin Eisenberg Washington University in St. Louis Arts Sciences | 2013 jeisenb...@wustl.edu jeisenberg...@gmail.com 262.914.4648 ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Amir M. Tahmasebi, Ph.D. postdoctoral researcher Rotman Research Institute, University of Toronto, Toronto, Ontario CANADA Tel: (416) 785-2500, ext. 3130 Web: www.cs.queensu.ca/~tahmaseb ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error while unzipping SuSE Itanium release
Hi there, I am getting the following error when unzipping the SuSE Itanium release: tar: Archive contains obsolescent base-64 headers Any help is appreciated. Thank you in advance, Regards, Amir -- Amir M. Tahmasebi, Ph.D. Medical Image Analysis Lab. School of Computing, Queen's University, Kingston, Ontario CANADA K7L 3N6 Tel: (613) 533-2797 Web: www.cs.queensu.ca/~tahmaseb ___ 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] error while unzipping SuSE Itanium release
Thanks a lot. It worked. Amir Krish Subramaniam wrote: Hi Amir 1. Try and check if the file you downloaded has the md5 checksum listed here -- http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/md5sum.txt For the Suse Itanium one, the string of characters you are looking for is e064d9a8b08dc10ecc57d1b60f0094f To find out the md5, use the command md5.. like md5 freesurfer-Linux-suse-ia64-stable-pub-v4.5.0.tar.gz enter 2. Searching a few internet forums, people have suggested the following might work. So try it out too gzip -d file.tar.gz and then do tar -xf file.tar -Krish On Apr 28, 2010, at 3:57 PM, Amir Tahmasebi wrote: Hi there, I am getting the following error when unzipping the SuSE Itanium release: tar: Archive contains obsolescent base-64 headers Any help is appreciated. Thank you in advance, Regards, Amir -- Amir M. Tahmasebi, Ph.D. Medical Image Analysis Lab. School of Computing, Queen's University, Kingston, Ontario CANADA K7L 3N6 Tel: (613) 533-2797 Web: www.cs.queensu.ca/~tahmaseb ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Amir M. Tahmasebi Ph.D. Candidate, Medical Image Analysis Lab. School of Computing, Queen's University, Kingston, Ontario CANADA K7L 3N6 Tel: (613) 533-2797 Web: www.cs.queensu.ca/~tahmaseb ___ 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] error running recon-all
Hi there, I am using the SuSE Itanium release and when running recon-all, I am getting the following error: mri_convert: cannot execute binary file Any clue? Thanks in advance, Regards, Amir Amir M. Tahmasebi, Ph.D. Medical Image Analysis Lab. School of Computing, Queen's University, Kingston, Ontario CANADA K7L 3N6 Tel: (613) 533-2797 Web: www.cs.queensu.ca/~tahmaseb ___ 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.
