Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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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retinotopic mapping with bowtie vs. wedge
by Y.V. Jiang 22 Nov '10

22 Nov '10

Dear Doug and other Freesurferers, We are considering using rotating bowtie-shaped stimuli rather than rotating wedges for retinotopic mapping. The bowties are essentially two symmetriccal wedges, but unlike horizontal/vertical meridian mapping, they do rotate around (rather that stay at horizontal/vertical meridian). Is Freesurfer's retinotopic mapping program capable of handling data analysis of bowtie retinotopy? Do we need to make changes to the analysis stream (e.g., when entering the number of cycles, should this be twice as frequent?) Would this mess up with color maps? Thanks for your feedback. -Yuhong ---------------------------------------------------------- Yuhong Vanessa Jiang, PhD, Department of Psychology, Univ of Minnesota jiang166(a)umn.edu, 612-625-7003 ----------------------------------------------------------

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severe recon-all errors only in v5.0
by Andreas Berger 22 Nov '10

22 Nov '10

Hello Surfers, we just finished processing our subjects (recon-all -all) with freesurfer version 5.0. In 16 out of 240 subjects i found severe errors: in about 4 of them the surface looks damaged (see attached screenshot1), in the others the skullstrip didn't work, in one case gnawing away some brain (see attached screenshot2), in the others there's too much skull left, the surface seems ok though (screenshot3). all of the 16 subjects looked fine with version 4.5. is this a known issue? by the way, recon-all reported no errors on any of them. will keep using v4.5 for now. thanks, andreas -- Andreas Berger <n0642496(a)students.meduniwien.ac.at>

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How to add volume to the pial surface?
by xuemei lei 22 Nov '10

22 Nov '10

Hi I have ran the recon-all using Freesurfer 5.0 version. And I found some GM tissue exluded from GM in temporal lobe like in the attached figure.I want to know how to fix these problems. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced the opposite problem, that is how to add volume. Thanks in advance！ -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning<http://psychbrain.bnu.edu.cn> Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 ============================================== Welcome to visit my blog: www.mobiye.com

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Re: [Freesurfer] volumetry of PSP related structures...
by antonio cerasa 22 Nov '10

22 Nov '10

Dear Gonzalo If you need to perform invidual evaluation I suggest you to consider the MR imaging index made by Prof. Quattrone (Radiology 2008, 246(1): 214-221). Overall, our FS results highlighted the role of thalamic atrophy in the patients with PSP. ----- Original Message ----- From: "Gonzalo Rojas Costa" <gonzalo.rojas.costa(a)gmail.com> To: <a.cerasa(a)isn.cnr.it> Sent: Saturday, November 20, 2010 10:24 PM Subject: Re: [Freesurfer] volumetry of PSP related structures... Hi: Which evidence you confirmed ?... you did the analysis of the volumetry of which structure ?... Culd you please send me the abstract of your work ?... I have a patient with PSP, and I processed the volumetry wirh freesurfer, but I don't know which structure must be studied... Sincerely, Gonzalo Rojas Costa El 20-11-2010 3:05, a.cerasa(a)isn.cnr.it escribió: > Dear Gonzalo > We've a PSP-freesufer paper in revision on Parkinsonisms and Related > Disorders. > In this particular population FS confirms evidence provided by previous > VBM studies. > > ----- Original Message ----- > From: Gonzalo Rojas Costa > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Fri, 19 Nov 2010 18:14:38 -0300 > Subject: [Freesurfer] volumetry of PSP related structures... > > Hi: > > How can I get the volume of pons, middle cerebellar pedunclues, > superior cerebellar peduncles ?... And, there exist any PSP-Freesurfer > related paper ?... > > Sincerely, > > -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- This message was scanned by ESVA and is believed to be clean. Click here to report this message as spam. http://smtp.isn.cnr.it/cgi-bin/learn-msg.cgi?id=0A23C28025.09A60

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