Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

VGL error
by Jason Tourville 01 Nov '11

01 Nov '11

Hello FreeSurferers, I run tksurfer remotely from a linux machine running CentOS (Boston University) using Virtual GL/TurboVNC. I have been able to do this successfully for years but have recently encountered the following error when calling tksurfer: surfer: tkoInitWindow(RMAUT015) [VGL] ERROR: OpenGL error 0x0502 [VGL} ERROR: in readpixels - - [VGL] 624: Could not Read Pixels The error occurs after the tksurfer image window is started but before a brain surface is displayed. I have confirmed that the error does not depend upon what ssh tunneling tool I am using nor on what time of machine I am using locally. Does anyone have experience with this problem? Suggested solutions? Cheers, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-6181 Fax: (617)353-7755

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Topology correction - segmentation fault
by Sindhuja Tirumalai Govindarajan 01 Nov '11

01 Nov '11

Hi all, I got the following error while running recon-all on a patient dataset. Kindly let me know how to proceed. Thanks! Sindhuja Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558 CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) Segmentation fault recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31 EDT 2011

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recon-all error
by Chindhuri Selvadurai 01 Nov '11

01 Nov '11

Hello, I am having trouble doing a recon-all of my data. pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i /cluster/archive/295/siemens/TrioTim-35006-20111026-155248-065000/364000-000015-000001.dcm -mail chinsel(a)nmr.mgh.harvard.edu' Here is the error: ERROR: no run data found in /autofs/cluster/manoach/dod/subjects/DODASD001/mri. Make sure to have a volume called 001.mgz in /autofs/cluster/manoach/dod/subjects/DODASD001/mri/orig. If you have a second run of data call it 002.mgz, etc. I usually do the recon all through launchpad first before any other preprocessing, and hadn't had a problem before? Not sure why this is the case this time. What step should be done before this to get the data in the mri? My subjects_dir is /cluster/manoach/dod/subjects Thanks so much!

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Hippocampal Sub-Field Segmentation -Appropriate Scan Protocol to Use
by Joshua Lee 01 Nov '11

01 Nov '11

Dear Experts, I've been collecting hi-res hippocampal scans with a 32 ch coil on a 3T Siemens Trio to manually segment hippocampal subfields. However, I wonder whether the protocol is appropriate for use with the new Freesurfer subfield segmentation tool. Specifically, our hi-res scan does not capture the entire brain, rather it acquires slices perpendicular to the long axis just for the length of the long axis axis. Can this scan be used for the new subfield auto-segmentation? Or does it require a whole-brain acquisition? We do acquire a 1 mm isotropic whole brain MPRage, but... Thanks for any info, Joshua

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Fwd: Position available: Postdoc in System and Cognitive Neuroscience - Beijing Normal University, China
by Zhen Zonglei 31 Oct '11

31 Oct '11

---------- Forwarded message ---------- From: Zhen Zonglei <zonglei.fsl(a)gmail.com> Date: Tue, Nov 1, 2011 at 11:13 AM Subject: Position available: Postdoc in System and Cognitive Neuroscience - Beijing Normal University, China To: FSL - FMRIB's Software Library <FSL(a)jiscmail.ac.uk> Postdoctoral positions are available to study the neural mechanisms of visual perception and cognition in the State Key Laboratory of Cognitive Neuroscience and Learning (SKLCNL), Beijing Normal University, Beijing, China. The SKLCNL (http://psychbrain.bnu.edu.cn) is one of the most influential institutes for brain research in China. The institute receives ample annual funding from multiple sources, including the Ministry of Science and Technology and the Ministry of Education of China; it also offers state-of-the-art research facilities incorporating new technologies, such as behavioral and molecular genetics, 3T fMRI, multielectrode recordings in awake behaving monkeys, optical imaging, TMS and EEG. Well-established PIs recruited overseas form a multidisciplinary research team covering the fields of cognitive neuroscience, psychology, neurobiology, computational neuroscience, information sciences and education. Dr. Jia Liu (http://psychbrain.bnu.edu.cn/teachcms/liujia.htm) studies the neural mechanism of object recognition and its heritability and experience dependency using multiple approaches such as psychophysics, fMRI and behavioral and molecular genetics. Dr. Wu Li ( http://psychbrain.bnu.edu.cn/teachcms/liwu.htm) studies intermediate-level visual processing, including top-down modulation and perceptual learning, in both humans and behaving monkeys. Candidates should have a doctoral degree related to neuroscience (including cognitive neuroscience and computational neuroscience) or psychology, and should have the ability to design and conduct experiments independently as well as to analyze fMRI or electrophysiological data. Strong computer skills including programming (MATLAB, Python, and C) are preferred. The SKLCNL offers competitive salaries depending on candidates’ previous training and experiences. If interested, please send a cover letter, a cv, a summary describing research accomplishments and interests, and the names and addresses of three references to Dr. Jia Liu (liujia(a)bnu.edu.cn) or Dr. Wu Li ( liwu(a)bnu.edu.cn) Zonglei Zhen

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Freesurfer November 2011