Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

preproc-sess error in version 5.0
by yuko YY 25 Nov '10

25 Nov '10

Hello, I recently switch to version 5, and am having a problem with preproc-sess in version 5.0. version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 OS : Mac 10.6.5 When I ran: preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold I got the following error: %-------------------------------------------------------------------------------------------------------------------------------------------- [Yukos-iMac:sessions/VM/VMan] yuko% preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ yuko setenv FREESURFER_HOME /Applications/freesurfer/freesurfer setenv SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/freesurfer/fsfast/bin/preproc-sess -per-session -fwhm 5 -force -surface VM20 lhrh -df sessdirfile -s VM20 -fsd bold Tue Nov 23 19:46:29 JST 2010 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain VM20 Template ----------------------------- mktemplate-sess -s VM20 -d /Users/yuko/Documents/FreeSurfer/sessions/VM -fsd bold Session: /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 ---------------- Tue Nov 23 19:46:29 JST 2010 find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found %-------------------------------------------------------------------------------------------------------------------------------------------- I found the same error reported in msg14982, but couldn't find a solution. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14982.html Can anyone tell me what I need to do to make this work? Yuko Yotsumoto % additional info -------------------------------------------------------------------------------------------------------------------------------------------- My data are at: sessions/VM/VM20/bold/001/f.nii sessions/VM/VM20/bold/002/f.nii .. sessions/VM/VM20/bold/009/f.nii and my study directory is at: sessions/VM/VMan/ subject is at: subjects/VM20 %--------------------------------------------------------------------------------------------------------------------------------------------

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"Invalid access of stack red zone"
by yuko YY 25 Nov '10

25 Nov '10

Hi, I'm having a java-related error with mkcontrast-sess. Are there any trick to get around this error? version: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 OS : Mac 10.6.5 javac 1.6.0_22 mkcontrast-sess -analysis VMfwhm5 -contrast all_null -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 -rmprestim % - (error message) --------------- Invalid capturehandle provided. No capture device associated with this handle !!! Opening log file: /Users/yuko/java.log.14247 Illegal instruction % --------------------------------------- more /Users/yuko/java.log.14247 % -------------------------------- Operating System: Darwin 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 Processor ID: x86 Family 6 Model 14 Stepping 5, GenuineIntel Host Name: Yukos-iMac.local Invalid access of stack red zone 0xb0105b2c eip=0x1fd64c % -------------------------------- Looks like a problem with java as discussed here: http://stackoverflow.com/questions/1501770/invalid-access-of-stack-red-zone… I've updated java, and got the same error. Thank you for your help! Yuko Yotsumoto

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Intracranial brain mask
by Tanner,Jared J 24 Nov '10

24 Nov '10

Hi, We want to control for intracranial volume in our analyses but we would like verify the reliability and validity of the ICV volume reported in the aseg.stats file (I know the methods reported on the WIki - http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV but haven't seen much in the way of a mask file we could look at). Is there an actual ICV mask file we can look at and load (and potentially edit)? Or, if not, is there an easy way to create an ICV mask? Thank you, Jared Tanner University of Florida

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Recon-all in 7 hours
by Pedro Paulo de Magalhães Oliveira Junior 24 Nov '10

24 Nov '10

Hi, I have recently tried the recon-all process in bert dataset in the new Amazon EC2 instance with a very powerful GPU. The results are very impressive: recon-all -s bert -use-gpu -all finished in 7hours and 15 minutes. It is a useful solution when you are in a hurry to finish some cases. It's a bit pricey: US$ 2.10 / hour It's supposed to run 8 cases simultaneously, but I didn't try it. Also I tried the Small EC2 instance and it can run a recon-all case in 27-35 hours with a cost of US$ 0.085 / hour. The advantage is that you can start hundreds of instances and finish your big study in one day if you can afford it :) cheers PPJ --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

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CUDA limit?
by Marcus N Schmidt 24 Nov '10

24 Nov '10

Hello, Is there a limit to how many processes can use CUDA at the same time? I just setup a new Linux workstation and am delving into FreeSurfer w/ CUDA. I'm getting the following error: Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : all CUDA-capable devices are busy or unavailable. Linux rietveld 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux Thanks, Marcus Marcus N Schmidt Erasmus MC Rotterdam, The Netherlands

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error while loading shared libraries:libGLU.so.1 during dt_recon
by xuemei lei 24 Nov '10

24 Nov '10

Hi, experts I ran the dt_recon and got a error like the follows: mri_probedicom --i /panfs/ hpc.bnu.edu.cn/home/leixuemei/DTI_recon/Raw/sub001/00001.dcm mri_probedicom: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory So, then I use LD_LIBRARY_PATH to add the libGLU.so.1. But this error still remained. is there someone ever met this error before？ Thank you in advance！ Xuemei --

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Paracingulate sulcus and registration
by Lena Palaniyappan 23 Nov '10

23 Nov '10

There has been some discussions previoulsy - but cant find a definitive answers. What is the implication of variability in Paracingulate sulcus in terms of Desikan and Destrieux parcellation schemes? In some disorders such as schizophrenia - about 16% variability has been reported. How is the ACC parcellated when PCS is absent, Hope someone can help Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Problems with --bg njobs flag in mri_glmfit-sim
by Adam Nitenson 22 Nov '10

22 Nov '10

Hi Freesurfer, I am using mri_glmfit-sim to run Monte Carlo simulations for a ROI specific region in my data. However, running 10000 simulations seems to go beyond the time limit for launchpad. I noticed the flag "--bg njobs : divide sim into njobs and put in background" in the description but am having trouble using it. I used the following command (Stable 4): mri_glmfit-sim --glmdir /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_56PatientsAndMatchedControls_Genotyped/RM_correct_error/CC_Minus_T/Monte_Carlo_LH_error_vs_correct_6sec_p01_56GroupLabel/ --bg 10jobs --sim mc-z 10000 2 mc-z.positive --sim-sign pos --overwrite and got the following error: (standard_in) 1: parse error nSimPerJob = while: Badly formed number. I tried other numbers, putting a space between the number and "jobs" and adding a decimal point but everything ends with the same error. How can I use that flag to divide 10000 simulations into, say, 10 jobs with 1000 each (assuming I am understanding the purpose of the flag correctly). Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Averaging 3d-MPRAGE images before processing
by Arman Eshaghi 22 Nov '10

22 Nov '10

Dear Freesurfer experts, We have acquired 2 sets of MPRAGE images in a single session to be averaged before processing in freesurfer. Is it valid if I use fslmaths command in fsl to average images and then feed the averaged image into freesurfer? Or do you recommend an equivalent of fslmath in freesurfer? I really appreciate your input on this issue. All the best, Arman

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mris_fix_topology error: "normal vector of length zero"
by Diandra Lucia 22 Nov '10

22 Nov '10

Hi all, I've searched the archives a bit, and found only one truly similar error which seems like it was never answered (that I could see, anyway). The case we're trying to process stopped during mris_fix_topology at this point: CORRECTING DEFECT 50 (vertices=22858, convex hull=4870) normal vector of length zero at vertex 153186 with 0 faces vertex 153186 has 0 face Numerical result out of range and then recon-all exits with errors. I checked the euler number, which seems high: eno=-988 (nv=200584, nf=403144, ne=604716) and the surface does report a very large number of defects: 166466 ambiguous faces found in tessellation segmenting defects... 185 defects found, arbitrating ambiguous regions... but from what I can see on orig.nofix, nothing seems really grossly wrong (i.e. no major skullstripping errors); from the defects labels, most of the defects seem to be in the sulci. I can send along the full logs if that would be helpful. Any advice? I'm using freesurfer-Linux-rh9-stable-pub-v4.2.0 Thank you, Diandra -- Diandra Lucia Research Assistant Project Coordinator INTRuST Neuroimaging Leadership Core Psychiatry Neuroimaging Lab, BWH 1249 Boylston St., Boston, MA 02115 email: diandra(a)bwh.harvard.edu phone: 617-525-6118

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Freesurfer November 2010