Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

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mri_convert multiple sequences
by Soon Hock Wei 25 Aug '10

25 Aug '10

2 1

How to add volume on pial surface in manual editting the trouble shootings
by 李瑾 25 Aug '10

25 Aug '10

Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. 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 another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin

3 4

CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/volumegpu_impl.hpp'
by DongHye Ye 25 Aug '10

25 Aug '10

Hi. folks. I'm trying to execute new cuda binaries in freeserfer 5.0. When I tried to run it (e.g. mri_em_register_cuda), I got the following error. ============================== ========================================================= Acquiring CUDA device Using default device CUDA device: GeForce 8500 GT aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading '/home/yed/Data/freesurfer_subjects/bert/mri/nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/volumegpu_impl.hpp' on line 104 : invalid argument. ======================================================================================== What am I missing? Please help me out. I appreciate your time. Regards, Dong

3 2

tkmedit and intensity normalisation
by Ali Radaideh 25 Aug '10

25 Aug '10

Dear FreeSurfer experts, I have two question for you please, First, I started recently to get the following message when I try to load the tkmedit GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: IP address And sometimes tkmedit.bin: xcb_io.c:452: _XRead: Assertion `dpy->xcb->reply_data != 0' failed. aborted Second, I have some images that have both intensity normalisation and Geometric distortion due to MS lesions. I followed the tutorial on how to fix these problems. My question is that, I don't want to re-run freesurfer twice (when I fix the intensity normalisation and one when I edit the white matter). Is there any command line I can use after saving changes to do both?. Many thanks in advance Ali 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.

3 2

Re: [Freesurfer] CUDA error
by orangekic 25 Aug '10

25 Aug '10

Hello, I am running FS V5.0 on personal computer outside the Martinos Center. The OS is CentOS 5.5, and the hardware is NVIDIA Geforce 8500 GT graphic card with latest driver (NVIDIA-Linux-x86_64-256.44.run). CPU: Intel(R) Core(TM)2 CPU 4400 @ 2.00GHz Thanks for your help. p.s. I made some mistake in the previous mail, which the CUDA toolkit 3.1 is for RedHat Enterprise 5.3. 2010/8/25 Help Desk Elf --- Chris Johnson <help(a)nmr.mgh.harvard.edu> What computer are you running this on? If you are doing this > from within the Martinos Center, we are having hardware problems with > the storage cluster on which freesurfer resides. > > > Hi, >> >> I have Install CUDA toolkit 3.1 (for Ubuntu Linux 9.10), >> 'fscudabins-linux-centos4_x86_64.tgz', and update the NVIDIA driver. >> And compiled as "recon-all -all -s subject1 -use-gpu" >> >> However, I got the CUDA error message: >> "CUDA error in file >> '/space/freesurfer/build/minerva/stable/dev/include/volmegpu_imp1.hpp' on >> line 104 : invalid argument." >> >> how can I solve this problem? >> >> Best, >> >> Kung. >> >> >> > > ------------------------------------------------------------------------------- > Chris Johnson |Internet: johnson(a)nmr.mgh.harvard.edu > Systems Administrator |Web: > http://www.nmr.mgh.harvard.edu/~johnson > NMR Center |Voice: 617.726.0949 > Mass. General Hospital |FAX: 617.726.7422 > 149 (2301) 13th Street |A lifetime is more than sufficiently long > Charlestown, MA., 02129 USA |to get what there is of it wrong. Piet Hein > > ------------------------------------------------------------------------------- > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

2 1

CUDA error
by orangekic 25 Aug '10

25 Aug '10

Hi, I have Install CUDA toolkit 3.1 (for Ubuntu Linux 9.10), 'fscudabins-linux-centos4_x86_64.tgz', and update the NVIDIA driver. And compiled as "recon-all -all -s subject1 -use-gpu" However, I got the CUDA error message: "CUDA error in file '/space/freesurfer/build/minerva/stable/dev/include/volmegpu_imp1.hpp' on line 104 : invalid argument." how can I solve this problem? Best. -- Yi-Chia Kung 龔怡嘉 Brain Connectivity Laboratory Institute of Biomedical Imaging and Radiological Sciences National Yang-Ming University Taipei, Taiwan Tel: +886 2 28267000 #6134

1 0

how to expand the disk size if I use VirtualBoxFS45
by Guang Zeng 24 Aug '10

24 Aug '10

Hi, there, I am using VirtualBoxFS45 now, everything is fine. But I find that after I load the FSVirtualBox.vdi, the default storage space is about 8GB. I'd like to use FreeSurfer to run multiple subjects (about 100), and then do group analysis using QDEC, however the 8GB disk space limit will be a big problem. Anyone know how to expand (or change) the default 8GB disk space in VirtualBox? Thanks a lot! Guang

2 4

CUDA error...
by Gonzalo Rojas Costa 24 Aug '10

24 Aug '10

Hi: I installed the latest NVIDIA driver (256.44) in my DELL Precision T3500 (Quadro FX-580 graphic board, Ubuntu 9.04)... Then I installed CUDA Toolit 3.1 (for Ubuntu 9.10)... Then, I restart my computer... I tried to process a study with the freesurfer command: "recon-all -autorecon1 -s ingrid -use-gpu", but I got the error: "/home/gonzalorojas/freesurfer/subjects/ingrid/mri mri_em_register_cuda -skull nu.mgz /home/gonzalorojas/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : unspecified driver error. Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all -s ingrid exited with ERRORS at Tue Aug 24 11:46:20 CLT 2010" How can I find a solution to that problem ?... Sincerely, Gonzalo Rojas Costa

2 1

From mgz to m3z
by Soon Hock Wei 24 Aug '10

24 Aug '10

2 1

Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 42
by Gonzalo Rojas Costa 24 Aug '10

24 Aug '10

Hi: Any solution for the 32 bit version ?... Sincerely, Gonzalo Rojas Costa > Message: 6 > Date: Fri, 20 Aug 2010 15:55:39 -0400 > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] CUDA Error - all CUDA-capable devices are > busy or unavailable > To: Daniel Guellmar <Daniel.Guellmar(a)med.uni-jena.de> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <1282334139.31414.17.camel(a)terrier.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8 > > CUDA users, > > The problem with the _cuda binaries (message: CUDA Error in file > 'devicemanagement.cu'...) has been fixed, and new binaries are available > for download from here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… > > download the file 'fscudabins-linux-centos4_x86_64.tgz' and extract it > (tar zxvf <filename>) into your $FREESURFER_HOME/bin directory. This is > for the 64b linux platform only (centos 4 and 5). > > fyi, the problem was that the utility UPX, which is run on the publicly > distributed freesurfer binaries to reduce their size, seemed to cause > this strange problem. > > Let us know how these utilities work. In particular we'd like to get a > sense of the type of NVIDIA GPU cards people are using. > > Nick >

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Freesurfer August 2010