Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

Can't locate a good link to 5.3-dev builds (Linux/Ubuntu or Neuro-debian)
by Shannon Buckley 28 Jun '16

28 Jun '16

Hiya, I'm trying to download a copy of your latest dev build for Freesurfer 5.3 - I'm interested in getting the latest build for Freeview for Linux/Ubuntu or Neuro-Debian - but I seem to keep getting an "unreachable site" message? ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev Is there another location I should be trying to use instead? Thank you very much for your time, Shannon T. Buckley Research Associate Fair Neuroimaging Lab Department of Behavioral Neuroscience and Psychiatry Oregon Health & Science University Mail code: L470 3181 SW Sam Jackson Park Road Portland, Oregon 97239-3098

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Research position, UCSF Department of Radiology and Biomedical Imaging
by Nick Schmansky, MGH 28 Jun '16

28 Jun '16

posted on behalf of Dr. Rahul Desikan: ============================= The UCSF Department of Radiology and Biomedical Imaging is looking for a researcher with strong interests in neuroimaging interested in a Specialist position at UCSF. We are a neurodevelopment and neuroimaging lab. Specialists (research assistant) appointed at the junior rank must possess a baccalaureate degree (or equivalent degree) or four years of equivalent research experience (e.g., with instrumentation and research equipment, social science research methods, or creative activities). Specialists appointed at the Assistant or Associate rank must possess a master’s degree (or equivalent degree) or at least five years of experience demonstrating expertise in the relevant specialization. Specialists appointed at the full rank must possess a PhD degree or ten or more years of experience demonstrating expertise in the relevant specialization. The ideal candidate will have 1+ years of lab experience (beyond coursework lab experience) and familiarity with one or more of the following: Matlab, R, Linux/Unix, C+ or other statistical or MRI image analysis software such as Freesurfer or FSL. We are seeking candidates with a strong background in neurosciences or biomedical engineering who have the ability to perform independent research in addition to supporting the lab. Candidates interested in working in the lab for at least 2 years are preferred. Combining neuroimaging, genetics and computational methods, we are primarily interested in elucidating mechanisms underlying neurodevelopment. Working in close collaboration with local collaborators at UCSF and investigators at UCSD, University of Oslo, and Harvard University/Martinos Center, the specialist will assist in a) developing a novel automated MRI atlas of the human brainstem and cerebellum, b) validating this hindbrain atlas on neuroimaging pediatric datasets with brain malformations, and c) organize and analyze our large database of pediatric neuroimaging and genetics datasets that we have in-house. UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. To apply, please provide the following materials to Dr. Rahul Desikan (rahul.desikan(a)ucsf.edu) 1) CV (must contain previous research experience) 2) Cover Letter - Short statement on why you are interested in this position and how this position will help you achieve your career goals 3) Three references

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QSM Hippocampal Segementation
by Jessica Sevick 28 Jun '16

28 Jun '16

Hello, I was wondering if it was possible to use the hippocampal subfield segmentation function (for FreeSurfer V 6.0) on QSM images? We are working on quantitative stratification of the hippocampus. If you could let me know any thoughts/suggestions that would be great. Thanks, Jessica Sevick MRI Research Assistant Seaman Family MR Research Centre T: 403.944.8652 C: 587.576.6666 Jessica Sevick T: 403.944.8652 C: 587.576.6666

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Longitudinal Stream: Recon-all and Base template
by Tamara Tavares 28 Jun '16

28 Jun '16

Hello All, I am planning to run the longitudinal stream on my data set and I have a few questions: 1) When I run the data cross sectionally using "recon-all -all" should I specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes individually through recon-all? My understanding is that some motion correction will occur if I specify more than one T1 which may alter the results versus if I specify one T1? 2) What input files should I use to create my base templates? Are the input files the norm.mgz files from each subject? Thank you in advance for your help! Best, Tamara

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recon-all sudden stop during Talairach
by Mikael Novén 28 Jun '16

28 Jun '16

Dear Freesurfer Developers, I'm attempting to process high resolution images on a new system and following https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I at first try to run downsampled (1x1x1 mm) images. recon-all suddenly stops during #@# Talairach with no error codes except for the "exited with ERRORS" message. I'm a bit clueless as to what could be wrong. The images are from a Philips 7T Achieva system and have been normalized using ANTS N4BiasFieldCorrectionImageFilter() before attempting recon-all (though uncorrected gives the same resulting error). I thought that there was a problem with the permissions so I changed the default using setfacl which seems to work but no change. OUTPUT: INFO: extension is mgz #-------------------------------------------- #@# Talairach tis 28 jun 2016 12:52:35 CEST /usr/local/freesurfer/subjects/106_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 106_1 exited with ERRORS at tis 28 jun 2016 12:52:36 CEST" BUILD-STAMP: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 OPERATING SYSTEM: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 16.04 LTS Release: 16.04 Codename: xenial UNAME -A OUTPUT: Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Log file included. Thank you very much for your help. All the best, Mikael Novén

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Download FreeSurfer
by Damien Marie 28 Jun '16

28 Jun '16

This message contained a link to a web site whose IP address has recently been associated with malicious activity. Due to that activity the site is not accessible from within the Partners Network. The link has been modified in the message below. If you feel this is an error please contact the IS Service Desk and open a ticket with the network security - phs assignment group. IS Service Desk numbers BWH 617-732-5927 BWH-RICS 617-525-0848 DFCI 617-632-3399 FALK 617-983-7454 LCC 857-307-4150 MCL 781-416-8940 MGH 617-726-5085 NHP 617-643-2020 NSMC 978-354-2014 NWH 617-243-6001 PCHI 781-433-3757 PHH 617-726-0790 PHS 617-726-5085 SRH 617-952-5555 ********************************* Hello everybody, Storage servers are offline for downloading FreeSurfer from the wikipage. Does anyone know an alternate location for the distribution please? Best, Damien

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updated mri_convert file
by Olivia Cheung 28 Jun '16

28 Jun '16

Hi Freesurfer team, I would like to download a copy of the updated mri_convert but the link <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes> on the Release Notes webpage does not seem to work. Would you please fix that? I need the updated mri_convert because I'm getting the following error: "nifti1Read(): unsupported slice timing pattern 5" Thanks! Olivia

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retinotopy analysis documentation
by Francesca Strappini 28 Jun '16

28 Jun '16

Hello Freesurfers, Where can I find the documentation about how is the retinotopic analysis performed in Freesurfer? Thanks. Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Freesurfer/Freeview help
by Abbie McNulty 27 Jun '16

27 Jun '16

Hello, I am trying to segment a MRI brain in order to create a mesh of the image into finite elements, but I am very new with Freesurfer/Freeview and am not familiar with the tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh this brain, how should I proceed? The online tutorials have confused me especially since I am not sure if I am supposed to be using the terminal or the command window for a lot of the code commands. Any help would be appreciated. Thanks! Abbie McNulty -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field

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Stuck on “CORRECTING DEFECT”
by Dan Loewenherz 27 Jun '16

27 Jun '16

Hi freeserver folks, First time poster here. First off, thanks so much to the folks who work on and make this software available to the public. It seems like pretty incredible tech, from what little I understand of it. :) My problem is that the freesurfer process appears to be stuck on the recon-all command. It’s been sitting at ”CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)” for about 10 hours now. Any way to cut that number down or should I just let it keep doing its thing? I’ve pasted all of the output pasted at end of the message. Thanks so much! Dan ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-684 (nv=141228, nf=283824, ne=425736, g=343) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... 190731 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 5 into 0 -merging segment 8 into 0 -merging segment 14 into 0 -merging segment 25 into 0 -merging segment 28 into 0 -merging segment 20 into 17 -merging segment 29 into 17 -merging segment 36 into 35 31 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8790 (-4.4395) -vertex loglikelihood: -7.4039 (-3.7020) -normal dot loglikelihood: -3.5029 (-3.5029) -quad curv loglikelihood: -6.1567 (-3.0783) Total Loglikelihood : -25.9425 CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)

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