Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Failed to download Freesurfer from ftp, server seems empty
by C. Minos Niu 29 Jun '16

29 Jun '16

Hello, I tried to have my new students download and install Freesurfer from https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall, but all download links gave "550 Failed to change directory" error. I logged into the FTP anonymously only to find it empty under "pub/". Any idea how to proceed with the downloading? Thanks! -Minos

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Diffusion MRI Workshop, 12-16 September, 2016
by Tim Dyrby 29 Jun '16

29 Jun '16

Dear Freesurfer users, Registration is officially open for the 4th ISMRM Diffusion MRI Workshop "Breaking Barriers in Diffusion MRI" to be held September 12-16 in Lisbon, Portugal! Dates: September 12-16, 2016 Venue: Sheraton Lisboa, Lisbon, Portugal Deadline for abstracts: July 21, 2016 Facebook: https://www.facebook.com/DSGworkshop2016/ As with the first three workshops held in 2002, 2005 and 2013, the workshop has been designed as the primary scientific venue for basic scientists and clinical researchers in the diffusion MR community to learn, meet the experts, discuss the latest advances in the field, and network. There is an optional bootcamp for trainees and those new to the field of diffusion MR on September 12. The formal scientific program from September 13-16 will cover the full scope of diffusion MR topics from acquisition to microstructure and modeling, anatomy, tractography, connectomics, validation, clinical application, and future strategies for innovation. Whether you are new to the field, a PhD student, postdoc, senior researcher or physician, we hope that you will be able to participate in the workshop and interact with the leaders in the field. *Please note that the deadline for scientific abstract submission is July 21, 2016.* For physicians in practice, the ISMRM is accredited by the ACGME to provide up to 25.75 AMA PRA Category 1 credits for participation in the workshop. For additional details, please visit the workshop website: http://www.ismrm.org/workshops/Diffusion16 or contact any of the organizing committee: / Mara Cercignani, Brighton & Sussex Medical School, Brighton, England, UK Maxime Descoteaux, Sherbrooke University, Sherbrooke, QC, Canada Tim B. Dyrby, Danish Research Centre for Magnetic Resonance, Hvidovre, Denmark Christopher Hess, University of California, San Francisco, CA, USA Alexander Leemans, University Medical Center Utrecht, Utrecht, The Netherlands / -- Tim B. Dyrby Associate Professor Danish Research Centre for Magnetic Resonance (DRCMR), section 714 Center for Functional and Diagnostic Imaging and Research Copenhagen University Hospital Hvidovre Kettegård Allé 30 2650 Hvidovre Denmark Office phone: +45 38626542 Mobile:+45 40790282 web: http://dig.drcmr.dk and www.drcmr.dk & Image Analysis and Computer Graphics section Department of Applied Mathematics and Computer Science Technical University of Denmark Richard Petersens Plads, Building 324 2800 Kongens Lyngby Denmark Office Phone: +45 45253424

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Problem while using the -localGI
by Hari Guragain 28 Jun '16

28 Jun '16

Dear Freesurfer experts, I am having trouble using the -localGI option to smoothen the pial surface. When I use the command like: recon-all -s ABC -localGI I got the following error: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-dev-20160611-876a0e6 cp: /Applications/freesurfer/subjects/ABC/scripts/lastcall.build-stamp.txt: Permission denied INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/ABC/scripts/recon-all.cmd: Permission denied. But when I tried to do the same reconstruction via the super user(su), it says something about the library linking like below. I am wondering if it is a problem related to Matlab or freesurfer? I am currently using the development version of freesurfer. Any help will be greatly appreciated. reading surface from lh.pial... dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Thank you all. Hari

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freeview display problem
by Ramtilak Gattu 28 Jun '16

28 Jun '16

Hello , I am having strange freeview display problem. The images doesnt appear in gray scale anymore. Please have a look at the attachment. Is there a switch that was turned on that I am not aware of. Could some one help. Thanks Regards Tilak

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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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