[Freesurfer] recon-all: Same MRI, different execution tame
Dear all, I'm performing a study about the variability of the execution time of recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for two identical MRIs (two copies of the same MRI), takes different execution time. I'm performing the execution using GPUs capability, but the same is happening for the CPU-only executions. Checking the output logs I found that in for example CA Reg, the number of the iterations is different, what's the main source of this variability? I guess that maybe It is related to some random seeds used and the convergence of the implemented methods. Am I right? CA Reg example: Execution Time 1 - Subject 1: 00:25:23 Execution Time 2 - Subject 1: 00:32:14 In both cases the computing node was used exclusively used for the recon-all execution. Did you measured the percentage of this variability? Can we extract some measures to compare the performed work on each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Fwd: Recon-all different execution time for same subjects
Dear freesurfer experts, I'm performing a study about the variability of the execution time of recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for two identical MRIs (two copies of the same MRI), takes different execution time. I'm performing the execution using GPUs capability, but the same is happening for the CPU-only executions. Checking the output logs I found i.e CA Reg, the number of the iterations is different, what's the main source of this variability? I guess that maybe It is related to some random seeds used and the convergence of the implemented methods. CA Reg example: Execution Time 1 - Subject 1: 00:25:23 Execution Time 2 - Subject 1: 00:32:14 In both cases the computing node was used exclusively for the recon-all execution. Did you measured the percentage of this variability? Can we extract some measures to compare the work realized in each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Fwd: Recon-all different execution time for same subjects
Dear freesurfer experts, I'm performing a study about the variability of the execution time of recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for two identical MRIs (two copies of the same MRI), takes different execution time. I'm performing the execution using GPUs capability, but the same is happening for the CPU-only executions. Checking the output logs I found i.e CA Reg, the number of the iterations is different, what's the main source of this variability? I guess that maybe It is related to some random seeds used and the convergence of the implemented methods. CA Reg example: Execution Time 1 - Subject 1: 00:25:23 Execution Time 2 - Subject 1: 00:32:14 In both cases the computing node was used exclusively for the recon-all execution. Did you measured the percentage of this variability? Can we extract some measures to compare the work realized in each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] recon-all complete in 10 hours!!!!
Hi Hassan, You can check my article Improving the execution performance of FreeSurfer : a new scheduled pipeline scheme for optimizing the use of CPU and GPU resources. http://www.ncbi.nlm.nih.gov/pubmed/24430512. By using the GPUS and a new workflow scheme, the execution time can be reduced to 4-5 hours. Additionally, if you use the scheduler we propose and you put a big workload to the scheduler, the execution time per subject should be reduced to 2h per subject, due to the increase of the throughput. Please have a look to the article and if you want to use the code, download it from github. If you produce some paper, cite me please. Best Regards 2015-06-12 22:15 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Hassan those numbers seem reasonable. If there is a big problem it will frequently take very long (due to giant topological defects) cheers Bruce On Fri, 12 Jun 2015, Hassan bakhshi wrote: Hi all, Recon-all complete in 10 hours,should i be concerned? I asked this question before, and Bruce said depend on your computer it is acceptable. i checked the hardware, I use virtual box which has 5 cores of cpu and 4GB of RAM. i ran 2 instance of recon-all and both finished within 10 hours. I have 4 pc like this which i'm running freesurfer on them and they finished within 10 hours for most of subjects and for some of them in 20 hours. I'm really concerned about the quality. If it is ok just make me relief. Kind Regards, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] recon-all CUDA error
Hi again experts, What version of CUDA was used to compile the *_cuda files, on the FS 5.3 stable version? Was it CUDA 5.0 or higher? /Jordi 2014-07-03 18:25 GMT+02:00 Chiu, Bryan (PHTH) bryan.c...@ubc.ca: Hi, I'm not sure which ones you want or are interested in. In the ~/freesurfer/bin/ you can find the mri_em_register_cuda as well as other *cuda binaries. In ~/Freesurfer/lib/cuda you can find some other files that may be of importance to you. I haven't had time to dig through them so far. Have you taken at look at the CUDA Developer's Guide wiki on the Freesurfer site? - Bryan -- *From:* Jordi Delgado [jordi...@pic.es] *Sent:* Thursday, July 03, 2014 12:36 AM *To:* Chiu, Bryan (PHTH) *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] recon-all CUDA error Hi again, Sorry I think that we have a missunderstanding. I was talking about the freesurfer mri_em_register_cuda and other mri_* binaries of freesurfer. Having the freesurfer files compiled in newer versions of cuda could include some optimizations at compiler level to run freesurfer processing in new architectures in the same way as you can compile the binaries for fermi support in the previous versions, there was a relevant improvement. I'm not sure if Kepler can't work with 5.0 or newer versions. I will talk with a more experienced fellows in CUDA programing and I will let you know... We keep in touch! 2014-07-02 21:13 GMT+02:00 Chiu, Bryan (PHTH) bryan.c...@ubc.ca: Hi, Thank you for your reply. The CUDA 5.x binaries can be found in the CUDA 5.x legacy drivers for CUDA. As long as you set the PATH=/usr/local/cuda/bin:$PATH and LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH, Freesurfer's cudadetect will look into here for the binaries. I think you should note that cudaDetect (belonging to nVidia) is different than Freesurfer's cudadetect (found in usr/freesurfer/bin). Apologies for the previous misconception. My issue right now is that the GTX 780 (kepler) cant work with 5.0. Do you know if it can work with 5.5? I might try my hand to see if I can compile for a newer version of CUDA. Keep me posted. - Bryan Hi there, I'm currently working on compiling FS source code trying to use CUDA 6, and newer GPUs like Titan series. I haven't got lucky yet, but I will keep on trying... In the meantime I would like to download the CUDA 5 binaries. Are these binaries been published? I can't find anything on the FreeSurfer wiki... In my previous work you mentioned Improving Execution Performance of FreeSurfer we used CUDA 3 binaries that I had compiled with --enable-fermi flag. Just to clarify your concern, we never used openmp on the test setup of that study, we have implemented a scheduler to manage K simultaneous recon-all executions. Thank you, 2014-07-02 19:06 GMT+02:00 Chiu, Bryan (PHTH) bryan.c...@ubc.ca: Hi, Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective lib64, you can pass the cudadetect for Freesurfer. However after it will crash with a segfault error. This leads me to believe that I installed correctly. I think Freesurfer only supports up to CUDA 5.0 so far (although I know Freesurfer group stopped supporting the option and left the flags around). Two options exist: Either in a future patch the program can just be enabled to call the newer version of CUDA (or if I can find where it tries to find CUDA from, edit it to accept any version), or to install any version of CUDA less than or equal to 5.0 To others: The OpenMP and -use-gpu flag are quite promising. I took a recon down from 12 hours to 3.5 hours using the -openmp 8 flag for a 4 core processor (i7 4770k). I am currently trying to see if I can speed up faster using the CUDA enabled option. There was a paper titled Improving the Execution Performance of Freesurfer which implements a resource scheduler on top of the CUDA and openMP option. No comment on the accuracy of the recon-all using all of these in combination. - Bryan Date: Mon, 30 Jun 2014 16:34:45 + From: Chiu, Bryan (PHTH) bryan.c...@ubc.ca Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: 680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.ca Content-Type: text/plain; charset=iso-8859-1 Hi all, I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed? My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get this to work. -Bryan Date: Fri, 27 Jun 2014 17:59:37 + From: Chiu, Bryan (PHTH) bryan.c...@ubc.ca Subject: [Freesurfer] recon-all CUDA error To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID
Re: [Freesurfer] recon-all CUDA error
to this tutorial ( http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/). With, of course some slight changes to install the latest toolkit. Thanks in advance, - Bryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] recon-all CUDA error
Hi there, I'm currently working on compiling FS source code trying to use CUDA 6, and newer GPUs like Titan series. I haven't got lucky yet, but I will keep on trying... In the meantime I would like to download the CUDA 5 binaries. Are these binaries been published? I can't find anything on the FreeSurfer wiki... In my previous work you mentioned Improving Execution Performance of FreeSurfer we used CUDA 3 binaries that I had compiled with --enable-fermi flag. Just to clarify your concern, we never used openmp on the test setup of that study, we have implemented a scheduler to manage K simultaneous recon-all executions. Thank you, 2014-07-02 19:06 GMT+02:00 Chiu, Bryan (PHTH) bryan.c...@ubc.ca: Hi, Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective lib64, you can pass the cudadetect for Freesurfer. However after it will crash with a segfault error. This leads me to believe that I installed correctly. I think Freesurfer only supports up to CUDA 5.0 so far (although I know Freesurfer group stopped supporting the option and left the flags around). Two options exist: Either in a future patch the program can just be enabled to call the newer version of CUDA (or if I can find where it tries to find CUDA from, edit it to accept any version), or to install any version of CUDA less than or equal to 5.0 To others: The OpenMP and -use-gpu flag are quite promising. I took a recon down from 12 hours to 3.5 hours using the -openmp 8 flag for a 4 core processor (i7 4770k). I am currently trying to see if I can speed up faster using the CUDA enabled option. There was a paper titled Improving the Execution Performance of Freesurfer which implements a resource scheduler on top of the CUDA and openMP option. No comment on the accuracy of the recon-all using all of these in combination. - Bryan Date: Mon, 30 Jun 2014 16:34:45 + From: Chiu, Bryan (PHTH) bryan.c...@ubc.ca Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: 680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.ca Content-Type: text/plain; charset=iso-8859-1 Hi all, I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed? My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get this to work. -Bryan Date: Fri, 27 Jun 2014 17:59:37 + From: Chiu, Bryan (PHTH) bryan.c...@ubc.ca Subject: [Freesurfer] recon-all CUDA error To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: 680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.ca Content-Type: text/plain; charset=iso-8859-1 Hi, I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I get an error as follows: [TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 Testing for CUDA device: /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what is going on? I setup CUDA and my Nvidia drivers according to this tutorial ( http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/). With, of course some slight changes to install the latest toolkit. Thanks in advance, - Bryan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
Re: [Freesurfer] Advice: Freesurfer Parallel Processing on Large Dataset
Dear Elijah, If I'm right, there are two options to accelerate FS execution: 1) The first option is using the FS openmp implementation http://surfer.nmr.mgh.harvard.edu/fswiki/OpenMP. I haven't tested this way but openmp allows to open multiple processing threads, and it is supported for the most time consuming steps of FS. 2) The second is using the GPU capabilities. This needs to have access to a GPU card, and add -use-gpu flag in your recon-all call. This activates the execution of the gpus implementations for CA Reg, SkullLTA, Inflation1 and so on, reducing the execution time (in my expertise, to 4-5 hours per subject). I recently developed a scheduler to optimize the FS workflow execution using the GPUs implementation and a left and right hemisphere steps in parallel. This will be published soon on the Springer NeuroInformatics journal. I hope that this will help a bit... Cheers, /Jordi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] CUDA binaries
Dear freesurfers, I'm trying to exploit CUDA capabilities by using recon-all with -use-gpu. On the freesurfer wiki I found an approximate speedups for the main CUDA implementations in Freesurfer ( http://ftp.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide). But I can't found mri_watershed_cuda and mri_ca_label_cuda on my freesurfer5.3/bin folder, and neither on previous versions. Are these implementations available? I tried to found the CUDA binaries on ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/) without luck. I know that CUDA support is no longer offered but it seems interesting to enable all the -cuda binaries executions to measure the improvement. And finally I would know if the cuda binaries offered in 5.3 version are compiled for a Fermi or Tesla? I hope that you are enjoying the summer! Kind regards, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] MRI artifacts detection
Dear FS experts, I'm studying the most common artifacts on MRI scanning. I started with the SNR calculation (which is included in recent FS versions), but I'm afraid that these artifact is filtered/processed with the scanner control program, and I'm wasting time trying to calculate this ratio. My qüestion is, any one of you know if the scanners control programs are correcting SNR, Inhomogeneties, motion, etc? Have any sense to detect these artifacts, as a quality assurance method before to accept/decline the adquired image with an external method of the scanner control program? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] MRI artifacts detection
Hi Bruce, Thank you for your fast answer. I'm focusing on SNR, Motion Correction and Intensity Inhomogeneities. Regards, 2013/5/13 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jordi this is definitely vendor specific. In Siemens you can for example turn on prescan normalization which will correct for intensity bias. You can have it generate two series - one with and one withour the correction. What other artifacts do you mean? There are lots of possibilities cheers Bruce On Mon, 13 May 2013, Jordi Delgado wrote: Dear FS experts, I'm studying the most common artifacts on MRI scanning. I started with the SNR calculation (which is included in recent FS versions), but I'm afraid that these artifact is filtered/processed with the scanner control program, and I'm wasting time trying to calculate this ratio. My qüestion is, any one of you know if the scanners control programs are correcting SNR, Inhomogeneties, motion, etc? Have any sense to detect these artifacts, as a quality assurance method before to accept/decline the adquired image with an external method of the scanner control program? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html 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/**compliancelinehttp://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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] mri_segstats SNR calculation
Dear Freesurfers, After running the first tests of freesurfer 5.2, I found a file named $hemi.w-g.pct.stats on the stats folder. The last column of the file is a SNR calculation, i found on the help manual, that is required to add --snr to perform this calculation. I'm interested to know how this SNR is calculated. Is there any method or paper related? Thank you in advance, /Jordi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] mri_segstats SNR calculation
Dear Freesurfers, After running the first tests of freesurfer 5.2, I found a file named $hemi.w-g.pct.stats on the stats folder. The last column of the file is a SNR calculation, i found on the help manual, that is required to add --snr to perform this calculation. I'm interested to know how this SNR is calculated. Is there any method or paper related? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Gray matter
Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calculated? Which structures are taken into account? Is there any file with this information Kind Regards, -- Jordi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Gray matter
Hi Gabriel, I will try it! Thank you! 2013/3/22 Gabriel Gonzalez Escamilla ggon...@upo.es Hi Jordi, I think you are looking for the information contained on the wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats *TotalGray* - total gray matter volume. This is simply the sum of SubCortGray + lhCortex + rhCortex + CerebellumGM. As such, it includes both surface-based volume calculations and voxel counts. To get a volume.mgz for the GM, you can use matlab and the aseg.mgz, or mri_extract_label, both with the number-IDs of the corresponding labels, as found in FreeSurferColorLUT.txt Cheers, Gabriel. El 22/03/13, *Jordi Delgado * jordi...@pic.es escribió: Dear FS experts, I have a double question about the gray matter calculations in FS: - Revising the aseg.stats, I noticed that there is a Total Gray Volume calculation. Is there a mgz volume with the gray matter? I cannot find it on the output mri folder... - How this total Gray Volume is calculated? Which structures are taken into account? Is there any file with this information Kind Regards, -- Jordi -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] cuda error...
HI Gonzalo, As Knut said, FreeSurfer is not compiled to run with CUDA 4. If you run ldd command to some freesurfer binary file you notice that the binary file links to libcudart.so.3 library. You should recompile the FreeSurfer source code. This is what I'm trying to do right now but is not easy and I haven't success yet... If someone has done it, please explain how... 2011/10/5 Knut J Bjuland knut...@hotmail.com Hi You should use Cuda 3.1 which is included with Freesurfer. Freesurfer is not compiled to use Cuda 4.0 or Cuda 4.1 Knut J Date: Tue, 4 Oct 2011 11:49:50 -0400 From: freesurfer@gmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cuda error... On Tue, Oct 4, 2011 at 11:15 AM, Gonzalo Rojas Costa gonzalo.rojas.co...@gmail.com wrote: I installed CUDA 4 in a Ubuntu 10.10 based workstation... I tried to process a volume, but I got the following error: writing output transformation to transforms/talairach_with_skull.lta... CUDA Error in file 'gcasgpu.cu' on line 159 : unspecified driver error. registration took 15 minutes and 1 seconds. Abort... I'm afraid I don't know what's going on there. I've never tried CUDA 4.0. Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] FreeSurfer Compiling error
Hi FreeSurfers, I'm trying to compile freesurfer with --enable-fermi-gpu and cuda 4. The process stopped with this error message: make[3]: Entering directory `/home/neuro/dev/mri_em_register' /usr/local/cuda/bin/nvcc -o em_register_cuda.o -c em_register_cuda.cu -arch sm_20 --ptxas-options=-v -g -I../include -I../include/dicom -I/home/neuro/mni/current/include em_register_cuda.cu(259): error: calling a host function(LinearGenerator::LinearGenerator) from a __device__/__global__ function(TransformLogps) is not allowed em_register_cuda.cu(262): error: calling a host function(LinearGenerator::LinearGenerator) from a __device__/__global__ function(TransformLogps) is not allowed em_register_cuda.cu(265): error: calling a host function(LinearGenerator::LinearGenerator) from a __device__/__global__ function(TransformLogps) is not allowed em_register_cuda.cu(269): error: calling a host function(TransformGenerator::TransformGenerator) from a __device__/__global__ function(TransformLogps) is not allowed 4 errors detected in the compilation of /tmp/tmpxft_7558_-4_em_register_cuda.cpp1.ii. make[3]: *** [em_register_cuda.o] Error 2 make[3]: Leaving directory `/home/neuro/dev/mri_em_register' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/neuro/dev/mri_em_register' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/neuro/dev' make: *** [all] Error 2 I don't know what is going wrong... Any idea? Thank you in advance! -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Error compiling freesurfer
/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(libutils_cuda_a-pgmstubs.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(libutils_cuda_a-const.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(gcamfots_cuda.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(gcamregisterlevel_cuda.o)' is incompatible with i386 output* em_register_cuda.o: In function `__gnu_cxx::new_allocatorstd::_Rb_tree_nodestd::pairint const, cudaDeviceProp ::allocate(unsigned long, void const*)': /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88: undefined reference to `operator new(unsigned long)' em_register_cuda.o: In function `__gnu_cxx::new_allocatorstd::_Rb_tree_nodestd::pairvoid (* const)(), cudaFuncAttributes ::allocate(unsigned long, void const*)': /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88: undefined reference to `operator new(unsigned long)' em_register_cuda.o: In function `__gnu_cxx::new_allocatorthrust::detail::device::generic::detail::element_pairfloat, long ::allocate(unsigned long, void const*)': /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88: undefined reference to `operator new(unsigned long)' collect2: ld returned 1 exit status make[2]: *** [mri_em_register_cuda] Error 1 make[2]: Leaving directory `/tmp/dev/mri_em_register' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/tmp/dev' make: *** [all] Error 2 It seems that there are some files that aren't compatible with 32 bits... 2011/5/25 Yaroslav Halchenko y...@psychology.rutgers.edu lacking -lXmu ? On Wed, 25 May 2011, Jordi Delgado wrote: ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU -lGL -L/usr/X11R6/lib -lX11 -lm ../glut/libglut.a -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib libtool: link: warning: library `/tmp/packages/mni/current/lib/[1]libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/[2]libminc.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/[3]libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/[4]libminc.la' was moved. g++ -o mris_show mris_show.o -L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib -L/usr/X11R6/lib ../utils/libutils.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU /usr/lib/libGL.so -lXext -lX11 ../glut/libglut.a -lz -lcrypt -ldl -lpthread /tmp/packages/mni/current/lib/libvolume_io.a -L/usr/pubsw/packages/mni/current/lib /tmp/packages/mni/current/lib/libminc.a -lnetcdf -lm -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils.a(pgmstubs.o)' is incompatible with i386 output ../glut/libglut.a(glut_cmap.o): In function `__glutSetupColormap': /tmp/dev/glut/glut_cmap.c:253: undefined reference to `XmuLookupStandardColormap' -- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
[Freesurfer] Download source code from repository
Hi Freesurfers, I'm trying to download the FreeSurfer's source code from de repository using: cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev and I obtain this message: cvs checkout: authorization failed: server fsvm.nmr.mgh.harvard.edu rejected access to /usr/fscvsroot for user anonymous Is there any problem with the repository? Thank you in advance! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] recommende pc and cuda
Hi Freesurfers, What Operating System are you using? I'm using CentOS 5.5 but with CUDA 3.2 and I have some problems with the nvidia.ko kernel module. Every time that I reboot the computer I have to make a modprobe and test with some CUDA SDK example... Other problems appear when I run multiple recon-all, often the processes crash with a kernel panic or simply with an abort. I don't know if the OS is interfering in the execution... Any idea will be apreciated... Thank you! 2011/4/5 Ian Malone ian.mal...@drc.ion.ucl.ac.uk On 05/04/11 16:55, Richard G. Edgar wrote: On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote: Richard G. Edgar wrote: On the standard test case we use here, a full recon-all run takes 8 hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins when using the Tesla C2050. Would I be right in concluding that a 4-core Nehalem (e.g. i7) has more throughput than the C2050 then? Yes, but less than having 3 CPU jobs, and one GPU one. I did test once, and there isn't much penalty to running one recon-all job per core on a Nehalem system. Right now, the CPU still does most of the work in the recon-all stream - it's something of a game of Amdahl's Law Wac-A-Mole. You could always try starting 4 GPU jobs at once I've not done the testing, but a C2050 would probably have enough RAM, and in any given recon-all run, the GPU does spend a lot of time idle. Hence, it would end up being divvied up between the four jobs. Thanks, that's interesting to know. -- imalone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] new GPU binaries
Hi Nick, Richard, Freesurfanados and GPU fans, I've downloaded the latest _cuda binaries from the tarball you have posted, but when I try to run the recon-all on the mri_ca_register_cuda it appears: * #...@# CA Reg Mon Oct 25 10:33:15 CEST 2010 /home/neuro/proc/OutPBS_GPU/AAG_106/mri mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/neuro/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : no CUDA-capable device is detected. ERROR: mri_ca_register with non-zero status 1 but continuing despite the error #-- #...@# CA Reg Inv Mon Oct 25 10:33:15 CEST 2010 /home/neuro/proc/OutPBS_GPU/AAG_106/mri mri_ca_register_cuda -invert-and-save transforms/talairach.m3z Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : no CUDA-capable device is detected. ERROR: mri_ca_register with non-zero status 0 Linux ww-neuro04 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AAG_106 exited with ERRORS at Mon Oct 25 10:33:15 CEST 2010* I think that error was solved in a previous releases of de _cuda binaries, maybe with the new compilation with cuda 3.1 it has been appeared again... I'm running cuda on a NVIDIA GEFORCE 9800 GT with cuda toolkit 3.2.9... Thank you!! /Jordi. 2010/10/25 Nick Schmansky ni...@nmr.mgh.harvard.edu Freesurfanados and GPU fans, We (namely Richard) have fixed some of the problems with the existing freesurfer gpu binaries, which were the result of building against cuda 3.0 on our build platforms, which seemed to be incompatible with 3.1. We've built against 3.1, although now i see nvidia has come out with 3.2, but i've tested against that and they seem to work. So you can get the binary tarball here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/fscudabins-linux-centos4_x86_64.tgz and here for the 32b linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/fscudabins-linux-centos4.tgz copy the extracted contents of those tarball into your freesurfer/bin dir. The binaries are: mri_ca_register_cuda mri_em_register_cuda mris_fix_topology_cuda mris_flatten_cuda mris_inflate_cuda mris_sphere_cuda mri_vol2vol_cuda No doubt people will encounter problems, so let us know. But hopefully you will see a dramatic reduction in the runtime of the subcortical segmentation stage (mri_ca_register). Also, to remind people, Richard is targeting our gpu development for the Fermi class of gpu card, which has better memory management which leads to better performance of some algorithms, so if you're buying new hardware, be sure to spec that class of card (see nvidia site). Nick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] recon-all using cuda
Hi FS experts, I'm currently testing FS v5 with cuda support. I'm using Centos 5.5 x86_64 on a DELL XPS with 4GB RAM, Intel Core 2 Extreme Processor QX9650 @ 3.67GHz and three GPUS Geforce 9800 GT. Every GPU has 512 GDDR3 memory, 256-BIT Memory Bus, 112 Stream Processing Units, 2x 400MHz RAMDACs and PCI Express 2.0 suport. The SDK examples runs perfect but when I run the following script: export FREESURFER_HOME=/home/neuro/freesurfer source /home/neuro/freesurfer/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/neuro/proc/OutPBS_GPU recon-all -all -force -i /home/neuro/orig/ACR_103/ACR_103_0002 -s ACR_103 -qcache *-use-cuda* I obtain the following error message: *** glibc detected *** mri_em_register: malloc(): memory corruption: 0x315dfdc0 *** === Backtrace: = /lib64/libc.so.6[0x3304072fae] /lib64/libc.so.6(__libc_calloc+0xcd)[0x330407495d] mri_em_register[0x42efad] mri_em_register[0x40e80d] /lib64/libc.so.6(__libc_start_main+0xf4)[0x330401d994] mri_em_register(__gxx_personality_v0+0x16a)[0x40b16a] === Memory map: 0040-00b55000 r-xp 0040 00:00 0 00b55000-00c54000 ---p 00b55000 00:00 0 00c54000-02627000 rwxp 00c54000 00:00 0 1ef6f000-3c61e000 rwxp 1ef6f000 00:00 0 [heap] 3303c0-3303c1c000 r-xp 08:03 79331333 /lib64/ld-2.5.so 3303c1c000-3303e1b000 ---p 3303c1c000 00:00 0 3303e1b000-3303e1c000 r-xp 0001b000 08:03 79331333 /lib64/ld-2.5.so 3303e1c000-3303e1d000 rwxp 0001c000 08:03 79331333 /lib64/ld-2.5.so 330400-330414e000 r-xp 08:03 79331340 /lib64/libc-2.5.so 330414e000-330434d000 ---p 0014e000 08:03 79331340 /lib64/libc-2.5.so 330434d000-3304351000 r-xp 0014d000 08:03 79331340 /lib64/libc-2.5.so 3304351000-3304352000 rwxp 00151000 08:03 79331340 /lib64/libc-2.5.so 3304352000-3304357000 rwxp 3304352000 00:00 0 330440-3304402000 r-xp 08:03 79331344 /lib64/libdl-2.5.so 3304402000-3304602000 ---p 2000 08:03 79331344 /lib64/libdl-2.5.so 3304602000-3304603000 r-xp 2000 08:03 79331344 /lib64/libdl-2.5.so 3304603000-3304604000 rwxp 3000 08:03 79331344 /lib64/libdl-2.5.so 330480-3304882000 r-xp 08:03 79331372 /lib64/libm-2.5.so 3304882000-3304a81000 ---p 00082000 08:03 79331372 /lib64/libm-2.5.so 3304a81000-3304a82000 r-xp 00081000 08:03 79331372 /lib64/libm-2.5.so 3304a82000-3304a83000 rwxp 00082000 08:03 79331372 /lib64/libm-2.5.so 3304c0-3304c16000 r-xp 08:03 79331354 /lib64/libpthread-2.5.so 3304c16000-3304e15000 ---p 00016000 08:03 79331354 /lib64/libpthread-2.5.so 3304e15000-3304e16000 r-xp 00015000 08:03 79331354 /lib64/libpthread-2.5.so 3304e16000-3304e17000 rwxp 00016000 08:03 79331354 /lib64/libpthread-2.5.so 3304e17000-3304e1b000 rwxp 3304e17000 00:00 0 330500-3305014000 r-xp 08:03 12817044 /usr/lib64/libz.so.1.2.3 3305014000-3305213000 ---p 00014000 08:03 12817044 /usr/lib64/libz.so.1.2.3 3305213000-3305214000 rwxp 00013000 08:03 12817044 /usr/lib64/libz.so.1.2.3 330640-3306409000 r-xp 08:03 79331382 /lib64/libcrypt-2.5.so 3306409000-3306608000 ---p 9000 08:03 79331382 /lib64/libcrypt-2.5.so 3306608000-3306609000 r-xp 8000 08:03 79331382 /lib64/libcrypt-2.5.so 3306609000-330660a000 rwxp 9000 08:03 79331382 /lib64/libcrypt-2.5.so 330660a000-3306638000 rwxp 330660a000 00:00 0 3309c0-3309c0d000 r-xp 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 3309c0d000-3309e0d000 ---p d000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 3309e0d000-3309e0e000 rwxp d000 08:03 79331394 /lib64/libgcc_s-4.1.2-20080825.so.1 330b40-330b4e6000 r-xp 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b4e6000-330b6e5000 ---p 000e6000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6e5000-330b6eb000 r-xp 000e5000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6eb000-330b6ee000 rwxp 000eb000 08:03 12824478 /usr/lib64/libstdc++.so.6.0.8 330b6ee000-330b70 rwxp 330b6ee000 00:00 0 2b2d46aaa000-2b2d46aad000 rwxp 2b2d46aaa000 00:00 0 2b2d46ab9000-2b2d47f2e000 rwxp 2b2d46ab9000 00:00 0 2b2d4800-2b2d48021000 rwxp 2b2d4800 00:00 0 2b2d48021000-2b2d4c00 ---p 2b2d48021000 00:00 0 7fff73ffe000-7fff741f2000 rwxp 7fe0a000 00:00 0 [stack] ff60-ffe0 ---p 00:00 0 [vdso] I attached the output log of the execution. Any idea will be apreciated! Thank you in advance!! -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona Tel: +34 93 586 82 32 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html INFO: /home/neuro/proc/OutPBS_GPU/ACR_103 exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /home/neuro/proc/OutPBS_GPU Actual FREESURFER_HOME /home/neuro/freesurfer -rw-rw-r-- 1 neuro neuro 34477 Oct 20 15:18 /home/neuro/proc
[Freesurfer] Missing structures lh.aparc.stats
Dear FS experts, We are using the 4.3.1 version of FreeSurfer, and we have noticed that in the lh.aparc.stats/rh.aparc.stats file there are 35 structures calculated and not 36 structures, only corpuscallosum is missing. We have also compared it with an old subject processing (using 4.0.2 version of FreeSurfer) where corpuscallosum structure has been calculated... Is this a known bug or maybe have we an error in our FS configuration or recon-all parameters? Thank you in advance, /Jordi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] QDEC Multigroupal analysis
Dear Experts, I'm trying to use QDEC for a Multigroupal analysis. I've read in the wiki that QDEC uses a GLM method to perform the analysis, but when I load a table with 43 subjects aprox. of three different groups and I run the analysis, at 70% QDEC shows me the following error: Error in Analyze: command failed: mri_glmfit --y ../path/qdec/qdecUntitled/y.mgh --fsgd ../path/qdec/Untitled/qdec.fsgd dods --glmdir ../path/qdec/Untitled --surf fsaverage lh --label ../path/fsaverage/label/lh.cortex.label Any idea? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edifici D E-08193 Bellaterra, Barcelona http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Fwd: FreeSurfer Error: bits = 0 not supported.
-- Forwarded message -- From: Jordi Delgado jordi...@pic.es Date: 2009/10/30 Subject: FreeSurfer Error: bits = 0 not supported. To: freesurfer@nmr.mgh.harvard.edu Hello*, * My name is Jordi Delgado, I work with FreeSurfer on a cluster of machines. Yesterday I sent some subjects to process and for three of them I recived in the Output Log from PBS the following message: * Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 INFO: SUBJECTS_DIR is /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS Actual FREESURFER_HOME /nfs/arpon/SOFTWR/freesurfer Linux td172.pic.es 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030 mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001... Starting DICOMRead2() dcmfile = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 dcmdir = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030 WARNING: tag ImageNumber not found WARNING: tag image orientation not found Ref Series No = 301 ERROR: bits = 0 not supported. Send email to freesurfer@nmr.mgh.harvard.edu Linux 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 29 18:26:01 CET 2009* After revising the freesurfer implementation and verify that other subjects have been processed correctly I noted that three subjects start their slices numeration with 0001 up to 0172 and the rest started (the correctly finished subjects) by 0002 up to 0171. So I searched this error in the freeSurfer wiki and google and I didn't found anything. What is happening? Is an image problem? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
