Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

full-time PhD position available -- DTI
by Jose Luis Cantero Lorente 29 Oct '09

29 Oct '09

The Laboratory of Functional Neuroscience at the Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Seville (Spain) invites applications for one full-time PhD student position to investigate on cerebral white matter integrity markers of healthy and pathological aging. The position is inmediately available, and the salary is according to spanish standards. Candidates will take a leading role in neuroimaging data analysis with a main focus on the development of novel analysis approaches to diffusion tensor imaging (DTI) data. Results will be integrated with structural MRI, FDG-PET and cortical neurophysiology from healthy aging and early stages of different neurodegenerative diseases. Applicants should have a degree in computer sciences, physics or applied mathematics. A computational/statistical background and good programing skills are essential (C/C++ and matlab). General interest in clinical neuroscience and cognitive function is considered important. To apply please email a detailed CV to Dr. Jose L. Cantero, e-mail: jlcanlor(a)upo.es Letters of recommendations will be required during the selection process. --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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cortical label values
by GREGORY R KIRK 28 Oct '09

28 Oct '09

Hi, I am using the cortical labels mapped into the aparc+aseg volume for seeding qball imaging. i looked around and did not find a complete listing of the numerical values of all the cortical parcellation labels. I can of course load the aparc on the surface in tksurfer and map them to the aparc+aseg volume with save point-go to point for each one but would save me some time to just have a list. i.e. the LUT and stats files just have the subcortical stuff. thank you Greg.

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how to install freesurfer on CentOS
by zhenxt03 28 Oct '09

28 Oct '09

Hello, would you please tell me where can I find the detailed steps to install the freesurfer on CentOS? Thank you in advanced!! Regard, Xiantong Zhen

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dual boot OS
by Ahmed, F, Me <fahmed＠sun.ac.za> 28 Oct '09

28 Oct '09

Hello, A quick question, if I wanted to run simultaneous recon-all jobs, would I have to install Linux as a dual boot operating system as opposed to what I currently have, which is an emulator? Thanks, Fatima

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qdec lauching error.
by Zhen Zonglei 28 Oct '09

28 Oct '09

Hi everyone: When I launched qdec in our system, I got the following error: X Error of failed request: GLXBadRenderRequest Major opcode of failed request: 151 (GLX) Minor opcode of failed request: 1 (X_GLXRender) Serial number of failed request: 1640 Current serial number in output stream: 1644 In my work, I access our linux sever remotely using VNC from a PC windows machine. Our Linux system is centos 4.0, and the version of FreeSurfer is 4.30. Any idea, how to resolve this problem? Thanks Zonglei Zhen -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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running fs on multi processing computers
by Ahmed, F, Me <fahmed＠sun.ac.za> 28 Oct '09

28 Oct '09

Hello FS experts, I have a large number of subjects to go through with running FS and I was wondering if there is any other way that I can speed this process up? Where I work, they have a "super computer" system where they can run parallel processing and I was wondering if Fs is able to run on such a system? I'm not too sure if that makes sense but I know the essence of it is to run a greater number of processing streams at one particular time. Thanks. Fatima

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postdoc position at MGH
by Bruce Fischl 27 Oct '09

27 Oct '09

Applicants are invited for a full-time Postdoctoral Research Fellow position. Responsibilities: Responsibilities will include two parts of a larger project. The first involves ultra high resolution MRI scanning of ex vivo samples and quantifying and optimizing the intrinsic CNR provided by different image contrasts (e.g. T1, T2, phase, etc...) The second involves algorithm development for registering structural acquisitions to histological scans and using function approximation/non-linear regression to approximate histology from MRI and vice versa. The fellow will become experienced in ultra high field MRI imaging and scanner sequence development as well as in multimodal imaging analysis. S/he will be expected to present findings at national meetings and compose related manuscripts. Environment: The fellow will interact with a number of faculty members at the Martinos Center, representing a diverse set of skills including Bruce Fischl, Andre van der Kouwe, Lilla Zollei and Larry Wald, and have access to world class imaging and computational facilities including human scanners (1.5T, 3T, 7T), small-bore scanners (4.7T, 9.4T, 14T, 15T) and high-performance computing (a cluster of 1200 cpus). Requirements: A PhD degree is required, preferably in computer science, bio-/ electrical engineering, physics or applied mathemetics. A strong computational/statistical background and good programming skills are essential (c/c++ and matlab). A general interest in brain research is important and Siemens IDEA programming skills are a bonus (but not required), as is some capability in hardware development/debugging. Some former experience with MRI analysis (especially with FreeSurfer/FS-FAST and/or SPM) and the Linux operating system can also be helpful. Contact: Please email Lilla Zollei, (lzollei(a)nmr.mgh.harvard.edu) each of the following items, preferably in a single file: (1) CV including GPA and a list of relevant courses; (2) description of previous research experience; (3) statement of research goals and interests; (4) three references The position is immediately available. The Massachusetts General Hospital is an Equal Opportunity/Affirmative Action Employer.

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Computer specifications for FreeSurfer
by smithtro＠comcast.net 27 Oct '09

27 Oct '09

Hello, I was wondering if the following specs on an IMac would meet the system requirements for FreeSurfer? 2.8GHz Quad-Core Intel Core i7 8GB 1066MHz DDR3 SDRAM - 2x4GB 1TB Serial ATA Drive ATI Radeon HD 4850 512MB 8x double-layer SuperDrive We are an outpatient facility and perform a good bit of Brain imaging on an older population and my Radiologists are interested in performing Brain volume for MCI and Alzhiemer Dementia patients. From the preliminary information that I read on the FreesurferWiki, the software application is very intensive and tends to run the computer system pretty rough. One of the biggest concerns would be the Graphics card? Is there a minimum memory spec (512mb or should it be higher)? Any help would be greatly appreciated. Regards, Bill William Smithtro RT(R)(MR) Chief MRI Technologist Laurel Highlands Advanced Imaging Johnstown PA www.LHAI.org

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glut
by Don Hagler 26 Oct '09

26 Oct '09

I recently started getting this error message when running tkmedit: GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context. This is with v4.4 on a machine running RHE5. Recent updates to RHE5 may be to blame. I get this error when running v3.0.5: freeglut (/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 143 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 37 Current serial number in output stream: 37 I see that there have been previous posts about similar errors, but I haven't found any replies with solutions. tkmedit does work when I use a different user account than the one I log into the xserver with. In that case, I get these messages: NVIDIA: could not open the device file /dev/nvidiactl (Permission denied). freeglut (/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): Unable to create direct context rendering for window 'Medit: ' This may hurt performance. Does anyone know of a solution for this problem? _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141665/direct/01/

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asegstats2table command not found
by Andrew Jahn 26 Oct '09

26 Oct '09

Hi, I am running FreeSurfer version 4.3, and when I type 'asegstats2table' I get a "command not found" error. I have my path set correctly (virtually all of the other commands in the freesurfer/bin directory work), but for some reason both asegstats2table and aparcstats2table do not. Any ideas? Thanks, -Andrew

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Freesurfer