Freesurfer May 2011

freesurfer@nmr.mgh.harvard.edu

120 participants
155 discussions

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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Beginner question
by David Grayson 26 May '11

26 May '11

Hey folks, I am totally new to freesurfer, so please forgive me… I am trying to open up an atlas in freesurfer that is in 4dfp.ifh format (or nii, if you like). Can anyone tell me how? Otherwise, I could try to reconstruct it straight from the T1 anatomical run, but when I try the following command, taken from the tutorial recon-all -i Scan_0002_Img_0160_MR.1.3.12.2.1107.5.2.32.35139.2011042716283971836201295 -subject 106382 –all I get errors at the nu_correct step, and it terminates. And I am running these commands in NX, if that makes any difference Thank you in advance for your help! David

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FreesurferEnv and matlab directory creation
by Peter J. Molfese 26 May '11

26 May '11

In the Mac version of Freesurfer, the FreeSurferEnv.sh script creates a matlab folder at ~/matlab. Can I change this location for running freesurfer on a grid (either Sun Grid Engine or Apple XGrid) where I won't always have access to a user folder? For instance, Xgrid runs jobs as an unprivileged user in a private directory (e.g. /private/var/xgrid/agent/tasks/TGSBflaF/working). Currently when I submit a job which sets up the freesurfer environment by calling the setup file and then a which to verify the environment is correct. The output shows that it executed the script and can now locate recon-all in /usr/local/freesurfer. But then I get a series of errors or warnings about matlab directory creation. Can I ignore these or silence them? Script: #!/bin/bash #setup Freesurfer export FREESURFER_HOME=/usr/local/freesurfer . $FREESURFER_HOME/SetUpFreeSurfer.sh which recon-all Output: INFO: /var/empty/matlab/startup.m does not exist ... creating /usr/local/freesurfer/bin/recon-all mkdir: /var/empty/matlab: Permission denied touch: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 213: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 214: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 215: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 216: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 217: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 218: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 219: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 220: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 221: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 222: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 223: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 224: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 225: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 226: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 227: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 228: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 229: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molfese(a)yale.edu

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Freesurfer May 2011