Freesurfer

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30132 discussions

CUDA Error - all CUDA-capable devices are busy or unavailable
by Daniel Guellmar 23 Aug '10

23 Aug '10

Hi folks, I'm trying to employ the new cuda binaries, which come with freesurfer version 5.0.0, however, if I'm trying to execute a cuda binary (e.g. mri_ca_register_cuda) I get the following output: Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : all CUDA-capable devices are busy or unavailable. This error occurs on two different systems which are cuda capable. Both systems run with Ubuntu 9.10, both have the latest developer driver for linux (256.40) and the latest cuda toolkit (3.1) on it. The GPU Computing SDK code samples compile and work fine. The device query on both hosts work fine ... see following output Host 1: CUDA Device Query (Runtime API) version (CUDART static linking) There are 2 devices supporting CUDA Device 0: "Tesla C2050" CUDA Driver Version: 3.10 CUDA Runtime Version: 3.10 CUDA Capability Major revision number: 2 CUDA Capability Minor revision number: 0 Total amount of global memory: 2817720320 bytes Number of multiprocessors: 14 Number of cores: 448 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 32768 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 1.15 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) Concurrent kernel execution: Yes Device has ECC support enabled: Yes Device 1: "Tesla C2050" CUDA Driver Version: 3.10 CUDA Runtime Version: 3.10 CUDA Capability Major revision number: 2 CUDA Capability Minor revision number: 0 Total amount of global memory: 2817982464 bytes Number of multiprocessors: 14 Number of cores: 448 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 32768 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 1.15 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) Concurrent kernel execution: Yes Device has ECC support enabled: Yes deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 3.10, CUDA Runtime Version = 3.10, NumDevs = 2, Device = Tesla C2050, Device = Tesla C2050 Host 2: CUDA Device Query (Runtime API) version (CUDART static linking) There is 1 device supporting CUDA Device 0: "Tesla C1060" CUDA Driv CUDA Runtime Version: 3.10 CUDA Capability Major revision number: 1 CUDA Capability Minor revision number: 3 Total amount of global memory: 4294770688 bytes Number of multiprocessors: 30 Number of cores: 240 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 16384 bytes Total number of registers available per block: 16384 Warp size: 32 Maximum number of threads per block: 512 Maximum sizes of each dimension of a block: 512 x 512 x 64 Maximum sizes of each dimension of a grid: 65535 x 65535 x 1 Maximum memory pitch: 2147483647 bytes Texture alignment: 256 bytes Clock rate: 1.30 GHz Concurrent copy and execution: Yes Run time limit on kernels: No Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously) Concurrent kernel execution: No Device has ECC support enabled: No deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 3.10, CUDA Runtime Version = 3.10, NumDevs = 1, Device = Tesla C1060 Any comments on that? Regards and thanks in advance, Daniel -- Dr.-Ing. Daniel Güllmar Medical Physics Group / IDIR I Jena University Hospital MRT-Gebäude am Steiger Philosophenweg 3 07743 Jena Tel: +49-3641-9-35373 Fax: +49-3641-9-35081 www: http://ww.mrt.uni-jena.de ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

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program error: Exec format error. Wrong Architecture
by Prisciandaro, James J 23 Aug '10

23 Aug '10

Hello list, I recently installed freesurfer on a dell laptop running centos 5.5. After installing successfully, I ran the suggested test commands on the freesurfer wiki (e.g., tkmedit bert orig.mgz; tksurfer bert rh pial; qdec). All returned the same error: Exec format error. Wrong Architecture. I googled this, and I noticed someone else was having a similar problem on August 9th 2010 and never got a reply from the list. I also saw someone getting a similar error in a non-freesurfer context, and it had something to do with their c compiler. My centos install is for the most part stock; and I'm not what you'd call a linux expert. Does anyone know what this is about? Thanks, Jim James J. Prisciandaro, Ph.D. Postdoctoral Fellow Department of Psychiatry and Behavioral Sciences Clinical Neuroscience Division Medical University of South Carolina 67 President Street PO Box 250861 Charleston, SC 29425 Ph (843) 792-1433 Fx (843) 792-0528

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CUDA Error...
by Gonzalo Rojas Costa 23 Aug '10

23 Aug '10

Hi Nick: I uncompressed the file "fscudabins-linux-centos4.tgz", but I continue to get the error: "mri_em_register_cuda -skull nu.mgz /usr/local/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 : CUDA driver version is insufficient for CUDA runtime version. Linux gonzalorojas-laptop 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s ingrid_2 exited with ERRORS at Fri Aug 20 21:48:43 CLT 2010" Could you please tell me how can I correct the problem ?... Sincerely, Gonzalo Rojas Costa Nick Schmansky escribió: > i've just posted the file 'fscudabins-linux-centos4.tgz' here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4/ > > note that we have recently discovered a new problem with running mri_em_register_cuda on brains with skull: the results are off compared to the cpu version. so updates to that will be available next week sometime. > > n.

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help unpacking raw files from CD
by tsporko＠nmr.mgh.harvard.edu 23 Aug '10

23 Aug '10

Hi, I have a problem unpacking raw files for data processing from the scanner from a read only cd (compact disk). When I try to unpack from /media/disk no such directory exits, yet I can cd into this directory. If I make a work directory for raw_data and cp from this read only disk I get an error that the .dat files cannot be read. Below is the unpacking command. Are you familiar with this? unpacksdcmdir -src ./ -targ ./ -scanonly scan.dat I am using the above command in (nmr-std-env) *note: if I used the unpack command of the files cp from the disk, I get the log file and the command initates reading the dicom files although I have the .dat error. Ideally I'd rather unpack directly from the CD. Has anyone had this error or trouble unpacking files from CD? Thank you! Tara

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a question about VirtualBoxFS4.5
by Guang Zeng 23 Aug '10

23 Aug '10

Hi, there, I am using VirtualBox45 now. After I installed it, I tested it using tkmedit and tksurfer command, everything looks ok. However, when I try to run a recon-all command, it fails at the mris_volmask step, the error mask I got is: "mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory" As someone suggested in the mailing list, I tried to make a symbolic link or a soft link named libtiff.so.3 which points to libtiff.so.4 using the following command: ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 ln -sf /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 But all of them gave me an error message: Permission denied. Does anyone can help? Thanks a lot! Guang

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Question about mri_ca_register Error when using recon-all
by huzhiwei＠sjtu.edu.cn 23 Aug '10

23 Aug '10

Hi all, I used recon-all of FreeSurfer to process data in NIfTi format. But I got an error message below about mri_ca_register. 0773: dt=0.014000, rms=0.427 (0.001%), neg=0, invalid=766 0774: dt=0.014000, rms=0.427 (0.001%), neg=0, invalid=766 0775: dt=0.014000, rms=0.427 (0.002%), neg=0, invalid=766 0776: dt=0.014000, rms=0.427 (0.001%), neg=0, invalid=766 0777: dt=0.014000, rms=0.427 (0.002%), neg=0, invalid=766 0778: dt=0.014000, rms=0.427 (0.001%), neg=0, invalid=766 Segmentation fault ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Mon Aug 23 08:48:28 CST 2010 /usr/local/freesurfer/subjects/ad2/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux ubuntu 2.6.32-24-generic #38-Ubuntu SMP Mon Jul 5 09:22:14 UTC 2010 i686 GNU/Linux recon-all exited with ERRORS at Mon Aug 23 08:48:28 CST 2010 The command I used is "recon-all -s subID -all -i /xxx/xxx...". The complete log can be found in attached file. What the problem it may be ? Would you please help me ? Thanks very much.

2 1

fwhm vs. fwhm-surf in version 5.0
by Shahin 22 Aug '10

22 Aug '10

Hi, In version 5.0 it is mentioned that "- fwhm-surf" is obsolete (I know it is still available). I want to know what "- fwhm" option exactly do when I have already mentioned that I want a surface only processing (by using "-surface self lhrh"). Does it do smoothing on the basis of volume or surface and how significant the difference is? Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

How to add volume on pial surface in manual editting the trouble shootings
by 李瑾 22 Aug '10

22 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

1 0

Binary masks from aparc+aseg.mgz
by Timothy Vickery 21 Aug '10

21 Aug '10

Hi all, I'm creating binary mask volumes in a subject's native functional space from the segmented brain in aparc+aseg.mgz (FS v 4.5). I have found that doing this two different ways produces different results, and I'm wondering if anyone can illuminate why this might occur and which method is more appropriate (or what other method you would suggest)... Method 1: Resample aparc+aseg.mgz into native functional space using mri_label2vol --seg aparc_aseg.mgz --fillthresh 0.5 [...plus the rest of the appropriate inputs such as subject's bold/register.dat] Then I just parse the resulting image (using matlab or python code) into separate binary masks for each unique identifier that I'm using...E.g., for right IPL I load this image and create a new volume [newVol = (oldVol==2008)] and save that out. Method 2: Create a label file from aparc+aseg.mgz for each unique identifier that I'm using, and then use mri_label2vol to produce a binary mask in native functional space: mri_cor2label --i aparc+aseg.mgz --id 2008 --l rIPL.label mri_label2vol --label rIPL.label --fillthresh 0.5 [... plus the rest of the required inputs, same as those used in Method 1] Even though these seem like they should be equivalent to me, and although the masks produced agree for the most part, I generally get several more voxels per ROI using Method 2 than I do using Method 1 (and not complete overlap otherwise). For instance, for one subject, Method 1 yields 308 voxels in rIPL, but Method 2 yields 316 voxels; disagreement between the two occurs in a total of 26 of those voxels, so it isn't just a matter of Method 2 being more generous. The discrepancy seems to be proportional to the size of the ROI, so I get just a handful of disagreements for smaller ROIs (but it seems to happen almost all the time). Thanks for any advice on which method is better, or a suggestion of a better method. Best, Tim

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ICV volume and 1.5T x 3.0T
by Tadeu Kubo 20 Aug '10

20 Aug '10

Hi FS, I have two important doubts... Is it the CSF volume included in the ICV volume (aseg.stats)? Is it possible include in the same group patient acquired from 1.5T and 3.0T? Do you have an article about this topic? TK

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