Freesurfer

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30132 discussions

PhD position in functional neuroimaging
by Michels Lars 31 May '11

31 May '11

PhD position in functional neuroimaging in patients with neurogenic and non-neurogenic lower urinary tract dysfunction Applications are invited for a doctoral research position in the human neuroimaging project "The bladder and the brain - supraspinal control of impaired lower urinary tract function in patients with neurogenic and non-neurogenic bladder dysfunction", funded by the Swiss National Science Foundation (SNF, 32003B_135774/1). Starting September 2011, we will investigate supraspinal lower urinary tract (LUT) control in patients with neurogenic (i.e. multiple sclerosis) and non-neurogenic bladder dysfunction. Patients with non-neurogenic LUT dysfunction will be investigated before and after therapy for their LUT dysfunction. The neuroimaging investigations will consist of a combination of advanced functional (functional MRI for resting state functional connectivity) and structural (diffusion tensor imaging (DTI) and voxel-based morphometry (VBM)) brain imaging methods. The candidate has the chance to participate in an innovative and multidisciplinary research project that is based on the long-standing successful collaboration and renowned scientific groundwork of the Institute of Neuroradiology at the University Hospital Zurich and the Neuro-Urology Research Group at the Balgrist University Hospital. The candidate should hold a Master's degree in neuroimaging, neuroscience, neurobiology, neuropsychology, neurophysiology, physics, or a related field. Fluency in spoken and written English and the ability to work within a multidisciplinary team are essential. Good oral German language skills are not mandatory but are advantageous. Experience with human MRI, or other brain imaging methods is an advantage. Familiarity with analysis software, such as SPM/Matlab or FSL, and experience with programming languages and statistical analysis is a great plus. Salaries are in accordance with the Swiss National Science Foundation (starting at around 40'000 CHF p.a.). For further information about the project please contact Dr. Lars Michels (lars.michels(a)kispi.uzh.ch) Your application includes your CV with a cover letter including a description of your motivation and research interests, a copy of your academic degree(s), and two academic referees to the address below. Reviews of applications will begin on 1 June 2011 and will continue until the position is filled. Dr. Lars Michels Department of Neuroradiology University Hospital Zurich Sternwartstr. 6 Zürich 8091 Switzerland

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going between scanner space and freesurfer space
by Trina Kok 30 May '11

30 May '11

Hi All, We would like to obtain a matrix to go from the orig.mgz/001.mgz space to freesufer space (i.e. that of T1.mgz, brain.mgz etc). I'm not sure which combination of vox2ras and ras2vox of the 2 volumes to extract to be able to obtain say for example, matrix T below. [orig.mgz (appended with ones for extra dimension] = T * [T1.mgz (appended with ones for extra dimension]; On a separate note, I'm using the affine function shown here in the below link to test out the transformations. The function does the interpolation by trilinear interpolation, and does rotation, shearing, scaling etc first, and the translation as a last step. http://www.mathworks.com/matlabcentral/fileexchange/21080. Is this the same or almost the same procedure used in going from scanner space to freesurfer space? Thanks a lot! Cheers, Trina

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cluster and FS new-version adaptation
by Alexandru Hanganu 30 May '11

30 May '11

Dear Freesurfer experts, 1) How many simultaneous processing can be done on a cluster ? I did 20 analysis at the same time, and it worked. They all finished without error. (didn't find this question on the list) 2) In order to adapt the previous subject analysing to the new FS-5.1, must I use the tags: -clean-bm -clean-tal (i.e. recon-all -subjid SUBJ -autorecon1 -clean-tal -clean-bm) Seems that the new analysis doesn't overwrite the previous data. Thank you in advance, Alex. * *

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Source code access
by Trina Kok 30 May '11

30 May '11

Hi all, I have an nmr center account and tried to checkout the FREESURFER source code. I logged in to door.nmr.mgh.harvard.edu via x-win, and then copied the following commands setenv CVSROOT /autofs/space/repo_001/dev cvs checkout -P dev but the following error appeared. I was wondering how should I go about looking at the code? Thanks! cvs checkout: failed to create lock directory for `/autofs/space/repo_001/dev/CVSROOT' (/autofs/space/repo_001/dev/CVSROOT/#cvs.history.lock): Permission denied cvs checkout: failed to obtain history lock in repository `/autofs/space/repo_001/dev' cvs checkout: Updating dev cvs checkout: failed to create lock directory for `/autofs/space/repo_001/dev/dev' (/autofs/space/repo_001/dev/dev/#cvs.lock): Permission denied cvs checkout: failed to obtain dir lock in repository `/autofs/space/repo_001/dev/dev' cvs [checkout aborted]: read lock failed - giving up

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correct mris_anatomical_stats syntax for cortical area
by Joakim Vinberg 27 May '11

27 May '11

Hi everybody, I just want to make sure I'm using the correct the correct syntax for running mris_anatomical_stats for examining cortical area. Based on the QDec Group Analysis page, my I was running the following command to examine cortical thickness: mris_anatomical_stats -l rh.test.label -t rh.thickness -b -f subject/stats/rh.test.stats subject rh To adjust this for cortical area, would I just replace the rh.thickness above with rh.area, or remove it entirely? Thanks in advance! Joakim

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FreeSurfer Tutorial and Workshop
by Eisenstein, Sarah 27 May '11

27 May '11

Does anyone know how to register for the FreeSurfer Tutorial and Workshop scheduled for September, 2011? I cannot find a link or a phone number to do this on the Course Description page (http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription) Thanks! Sarah Sarah A. Eisenstein, Ph.D. Postdoctoral Scholar Hershey Lab Psychiatry/Neuroimaging Lab Washington University in St. Louis St. Louis, MO eisensteins(a)npg.wustl.edu

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cerebellum atlas template
by Anthony Dick 27 May '11

27 May '11

Hello all, We are looking to develop a cerebellum atlas training set based on the Schmahmann et al (2000) parcellation so we can automatically segment the cerebellum based on this atlas. Does this exist already? I know Makris and colleagues had done something similar to this, but I am not sure if it has been developed for Freesurfer. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick

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ris_fix_topology malloc error in FS5.1
by peter.molfese＠yale.edu 27 May '11

27 May '11

I was processing a particularly noisy participant which bombed out with the following error. Looking at the data, it shouldn't make it through the pipeline, but the error message seems more of a memory management issue. I've pasted it below, any thoughts? Freesurfer 5.1 (new build), Mac Pro Workstation with 40GB RAM, Mac OS X 10.6.7 Error Message: CORRECTING DEFECT 48 (vertices=60474, convex hull=11331) mris_fix_topology(23279) malloc: *** mmap(size=3887681536) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Excessive topologic defect encountered: could not allocate 242979990 edges for retessellation Cannot allocate memory Darwin ella.haskins.yale.edu 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:16:10 PST 2011; root:xnu-1504.9.37~1/RELEASE_X86_64 x86_64 recon-all -s sn3086 exited with ERRORS at Thu May 26 22:47:37 EDT 2011 For more details, see the log file /zappa/freesurfer/PID/sn3086/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Freesurfer 5.1 - ERROR: talairach_afd
by Yiyu Chou 26 May '11

26 May '11

Dear Freesurfer Users, I tried the freesurfer 5.1 using command "recon-all -i xxx -s xxx -all" but I got an error message that didn't happen with version 5.0 on the same subject. "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***" Is it normal ? YY

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Re: [Freesurfer] I/O performance mitigation
by Bruce Fischl 26 May '11

26 May '11

Hi David, I'm surprised you didn't have to do this in the past. We always space our jobs out. Glad there's an easy workaround cheers Bruce On Fri, 3 Sep 2010, David Mischel wrote: > We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all > jobs. The attached Word doc (I don't know how to contribute this information > other than attaching the image and text using Word) shows a load graph on > our file server. When 20 FS jobs began at once (all processing servers using > a single file server) the load on the file server bulged up. When we spaced > out the launch of each job by 15 seconds the load hardly budged. > > > > We have not had to do this in the past with earlier versions of Freesurfer > but this is an obvious work around to the problem we encountered. > > > > < david > > > > > > David Mischel > > Manager of IT > > Center for Imaging of Neurodegenerative Diseases (CIND) > > <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ > > VA Medical Center > > 4150 Clement Street, 114M > > San Francisco, CA 94121 > > voice: 415-221-4810 x3864 > > fax: 415-668-2864 > >

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