Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

tutorial_data
by bruno fraccini pastorello 29 Jun '16

29 Jun '16

Dear freesurfer support,I'm trying to download the freesurfer data to learn freesurfer, but i can't it. Do you know why? Could you help me? I tried use this link ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I obtain this error: Safari cant open the page ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz because Safari can't load any data from this location. Thanks in advanceBruno Pastorello PS: I tried use this link too :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data using curl command on terminal and it has failed too

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checking freesurfer output
by Gabor Perlaki 29 Jun '16

29 Jun '16

Sorry to repost my question. I would appreciate any reply. Best Regards, Gabor 2016-06-13 10:51 GMT+02:00 Gabor Perlaki <petzinger.gabor(a)gmail.com>: > Dear all, > > I've a lot of patients and we are looking for the fastest solution to > check the output of Freesurfer. On the troubleshooting page ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) > there are a lot of steps to check, but I think not all of that should be > done to find out whether there is error in the final segmentations. > I think, but I am not sure, that checking the surfaces (white and pial) > and checking the subcortical segmentations (aseg) is enough to realize if > something is wrong. After an error is detected based on the checked outputs > (surfaces and aseg), we can find out the exact nature of the error and > correct it based on the troubleshooting page. Is it a good solution for > verifying the performance of Freesurfer by checking only these two things > (surfaces and aseg) or I need to check all of the steps listed on the > troubleshooting page anyway? > > > Best Regards, > Gabor > > <petzinger.gabor(a)gmail.com> > -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor(a)gmail.com

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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

1 0

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

2 1

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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Freesurfer