Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

Statistical output
by mmoayedi＠uhnres.utoronto.ca 29 Oct '09

29 Oct '09

Hi everyone, I was hoping you can clarify something for me. I'm comparing two groups using CTA (in freesurfer). When I set up my model, I include age as a covariate of no interest. To do this, I include it as a variable in the fsgd, and in the contrast matrix, I regress out the effects of age, by setting the vectors to 0. However, when I extract the results from the analysis (the thickness values), and graph them against age, I find that I have an interaction, or an age effect nonetheless. Could you please shed some light on this for me? Thanks, Massih

2 1

problem starting qdec
by Dana W. Moore 29 Oct '09

29 Oct '09

Hi everyone, I am trying to use qdec for the first time, and I get the following error message: X Error of failed request: GLXBadRenderRequest Major opcode of failed request: 132 (GLX) Minor opcode of failed request: 1 (X_GLXRender) Serial number of failed request: 1705 Current serial number in output stream: 1709 Locking assertion failure. Backtrace: #0 /usr/lib/libxcb-xlib.so.0 [0x4455a767] #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x4455a81e] #2 /usr/lib/libX11.so.6 [0x4033d518] #3 /usr/lib/libX11.so.6(XESetCloseDisplay+0x31) [0x403208d1] #4 /usr/lib/libGL.so.1 [0x40291b69] I am accessing our linux computer remotely using ssh from a windows machine--I don't know if this is related to the problem. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

4 6

Surface errors
by Evert van Velsen 29 Oct '09

29 Oct '09

Hi, I am trying to reconstruct the surfaces of 1.5T images that I have (n>800). In almost half of my images, minor portions of the temporal and orbitofrontal lobes are missing (e.g. see images attached). Has somebody any suggestions how to solve this problem in an easy way (FreeSurfer settings e.g.), as it is (almost) impossible to add control points for all subjects. Thanks, Evert

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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.

2 1

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

1 0

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

3 3

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

1 0

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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Freesurfer October 2009