[Freesurfer] FreeView updating
Hello, I would like to download the latest version of FreeView so I could use the Recon Edit option. I've downloaded the latest version of FreeSurfer (v5.3), but it seems that I have an older version of FreeView (v1.0). Could someone please assist me in updating FreeView - I can't find the download for it. Regards, ___ Bryan Chiu Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ 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] dt_recon image inputs -i flag
Hi, I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI images in par/rec. I ran dcm2nii and have retrieved the associated *bval, *bvec and *nii.gz files that come out. In the tutorial it mentions the -i flag requiring a dcm image. Is it possible to pass a *.nii.gz file ? Regards, ___ Bryan Chiu Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ 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] freeview data checking for longitudinal
Hi, I am trying to create a command line for data checking the same participant over multiple longitudinal timepoints in freeview. However at the moment I am running into issues. Can someone provide me an example of a freeview command to be used if I wanted to overlay the scans? Any help is greatly appreciated. ___ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ 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] Overclocking CPU for Freesurfer
Hi, Is anyone aware of any issues that arise from overclocking and using Freesurfer? I was looking to see how much it would speed up recon-all with OpenMP using a stable overclock. ___ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ 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] Functional Overlay onto Structural
Hi, I need to overlay some functional imaging data onto a structural scan to create some figures. How would I do this? I tried an older tutorial but it seems the files don't exist anymore in the tutorial dataset (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization). However the image provided is what I would like to create as a figure. It is not necessary to overlay onto the participants brain and could easily get away with overlaying it on a standard brain. I was given analysis files from FSL. Namely the one I was told to overlay was *.nii.gz file following the FEAT analysis from FSL. Regards in advance. ___ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ 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, The *_cuda included in Freesurfer 5.3 is compiled for 5.0. I do not think CUDA 5.0 supports Kepler cards. The lowest CUDA version supported by my GTX 780 is CUDA 5.5 From: Jordi Delgado [jordi...@pic.es] Sent: Tuesday, July 08, 2014 6:54 AM To: Chiu, Bryan (PHTH) Cc: freesurfer@nmr.mgh.harvard.edu Subject: 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.camailto: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.esmailto:jordi...@pic.es] Sent: Thursday, July 03, 2014 12:36 AM To: Chiu, Bryan (PHTH) Cc: freesurfer@nmr.mgh.harvard.edumailto: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.camailto: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.camailto: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.camailto:bryan.c...@ubc.ca Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.camailto
Re: [Freesurfer] recon-all CUDA error
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.camailto: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.camailto: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.camailto:bryan.c...@ubc.ca Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.camailto: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.camailto:bryan.c...@ubc.ca Subject: [Freesurfer] recon-all CUDA error To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer
Re: [Freesurfer] recon-all CUDA error
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.
[Freesurfer] (no subject)
Hi Chris, If you could get support for CUDA 5.5 it would be marvelous. I'm quite inexperienced with the CUDA programming (consider me an enduser), you would have my full support. I also have a computer here to do any testing if needed. I have a PC with CentOS 6.5, Freesurfer 5.3.0, i7 4770k, 16 Gb RAM, GTX 780.. etc. On that note I have been trying to replicate the methods and the scheduler introduced in Improving the Execution Performance of Freesurfer by Delgado et al. . Let me know if you need any help or would like to collaborate. -Bryan Date: Wed, 2 Jul 2014 03:46:01 + From: Chris Adamson chris.adam...@mcri.edu.au Subject: Re: [Freesurfer] Build with CUDA 5.5? To: Z K zkauf...@nmr.mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 43a4603348d2ac409b1b958efe5c8b940118273...@mitsmxmbx02v.mcri.edu.au Content-Type: text/plain; charset=us-ascii I understand about matching all the different combination of driver versions with linux distros. My plan is to use a centos 6.5 distro and just install the CUDA 5.5 library. I will try and replicate what there is already with CUDA 5.0 with the new library. I will let you know how it goes. I understand about not having resources to devote to a programming task. The CUDA versions are still definitely worth since they are faster than the CPU versions even after openmp and they don't force you to hog all the CPU cores. -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, 2 July 2014 1:41 AM To: Freesurfer support list; Chris Adamson Subject: Re: [Freesurfer] Build with CUDA 5.5? Chris, This is why we no longer actively support CUDA development in freesurfer and instead have focused on openmp to reduce overall runtime. The complexity of the CUDA programming coupled with the required libraries/driver matching of various builds with various OSes is simply beyond the resources we have to devote to the task. As you know, we currently build against CUDA 5.0, and if your OS supports it, you can run the more computationally intensive tasks (mri_ca_register, etc) using CUDA. Beyond that you are free to attempt a build of the freesurfer source code against the CUDA 5.5 on your Ubuntu system. I can assist with that task by providing the other 3rd party libraries as well as general insight, but beyond that we simply do not have the resources to devout to that task. -Zeke On 06/30/2014 10:19 PM, Chris Adamson wrote: Guys, Would it be possible to get Freesurfer 5.3.0 built with CUDA 5.5? The newest Ubuntu does not have support for 5.0. Thanks in advance, Chris Adamson. *Dr **Chris Adamson *Research Officer, Developmental Imaging, *Murdoch Childrens Research Institute *Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.auhttp://www.mcri.edu.au http://www.mcri.edu.au/ E chris.adam...@mcri.edu.au T 03 9936 6780 __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com __ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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, 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.camailto: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.camailto:bryan.c...@ubc.ca Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.camailto: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.camailto:bryan.c...@ubc.ca Subject: [Freesurfer] recon-all CUDA error To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.camailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo
Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH))
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.
[Freesurfer] recon-all CUDA error
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.
Re: [Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint
The output brain is that which I see from freeview. I usually check their sulci and gyri to confirm if a scan is good. I resolved the issue by rerunning my PAR/REC files through the same dicom to nifiti converter for all of them. It turns out the person before me used a different tool which resulted in incongruent scans of the same participant through multiple timepoints. Thanks, - 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.
[Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint
Hi, I'm attempting to do some longitudinal processing on a set of data with subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 12 months after Final. When visually checking over a subject in Freeview, I notice that all of my Midpoint runs are left-right flipped, where the other 3 timepoints' scans are congruent with one another. What can I do to flip these Midpoint volumes left-right before I rerun them all in recon-all -all? As well, since these are going to the same subjects for my longitudinal design in creating a 'base' file we have to ensure that we maintain the same orientation of the brain across all timepoints (left-right)? 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.
Re: [Freesurfer] Why the result was not same for the same subject
There of course is some variability in the analysis due to the way the segmentation happens. Your results are certainly not out of the ordinary for the volume you are viewing. On average you can expect a ~1% variance between several scans of the same subject. If you want to know more I certainly suggest reading the paper titled: Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain - 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.
Re: [Freesurfer] CUDA problem with FreeSurfer 5.3.0 on CentOS6
Bump. Having the same problem with a similar setup. ___ 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] Differing OS X version and recon-all
Hi, Wanted to check in about Mac OS X and any effects on recon-all that I may not be aware of. A while back the Mac was updated to 10.9.2 from some other version of 10.x.x. I ran half of my recon-all on 10.x.x, and am running my 2nd half on 10.9.2. The update was due to some IT person thinking the older version had security flaws. Will I need to rerun all of my subjects on 10.9.2, or has there been no reported differences between these two versions? Thanks, - 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.
[Freesurfer] CUDA PC build
Hi, Trying to build a CUDA enabled PC for the lab to do processing for a variety of neuroimaging programs including Freesurfer and FSL. Want to know input from others about the 'recommended' PC and what the 'standard' is based on the current PC prices and technology. Sample build is from NCIX Canada, if curious. SKU Description Price Amount 84500 ASUS Z87-A ATX LGA1150 Z87 DDR3 3PCI-E16 2PCI-E1 2PCI CrossFireX/SLI SATA3 USB3.0 HDMI Motherboard [Reg. $159.99] $154.99 $154.99 93608 ADATA Xpg V1.0 16GB DDR3-1600 CL9-9-9-24 2X8GB Dual Channel Memory Kit Black [Reg.$189.99] $149.99 $149.99 82953 ASUS DRW-24F1ST 24X SATA DVD Writer Black $24.98 $24.98 65701 Seagate Barracuda 1TB 7200RPM 64MB SATA 6Gbps 3.5in Internal Hard Drive - OEM [Reg. $73.44] $64.99 $64.99 76367 ASUS GeForce GTX 660 OC DirectCU 1020MHZ 2GB 6.0GHZ GDDR5 2xDVI HDMI DisplayPort PCI-E Video Card $229.99 $459.98 81327 Intel Core i5 4670K Unlocked Quad Core 3.4GHZ Processor LGA1150 Haswell 6MB Cache Retail [Reg. $269.98] $249.99 $249.99 38650 Corsair Professional HX850W 850W ATX 12V 70A 24PIN ATX Modular Power Supply Active PFC 140mm Fan $169.98 $169.98 67326 Antec Three Hundred Two Mid Tower Gaming Case 302 ATX 3X5.25 6X3.5INT No PS Front USB3.0 Audio [Reg. $77.98] $69.99 $69.99 In short -- runs with 16 Gb RAM, 3.4 GHz Quad core, with 2 GTX 660s in SLI. Final quote comes out to $1506 CAD. This is my first time attempting to build a PC of this type, so I still have tons of questions regarding minor details. I think spec wise the computer is good, unless others have recommendations from previous experience. Most likely will be running a flavour of Linux on this rig. Any suggestions for what the 'standard' for this build would be? I'm thinking CentOS based on older webmail threads, but I would prefer Ubuntu if possible. I would also like it to be user friendly so the technologically challenged researchers can get the software up and running. Is there anything else I should think about before I order? I want to make sure I have all of my bases covered before ordering and getting this rig going. Regards, - Bryan Chiu ___ 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] Incorrect orientations from MRI convert
Hi Douglas, I've looked at the original images in freeview and they follow the correct talairach coordinates. I've run mri_convert again and the files follow the correct talairach coordinates. It appears this may have been a 'one-off' issue. Will update after I autorecon everything. - 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.
[Freesurfer] Incorrect orientations from MRI convert
Hi, I am working on a dataset using free surfer. I have NIFTII files which I am converting using mri_convert. Upon completion of mri_convert, the orientations of the files are wrong. This likely leads to an incorrect talairach (I was getting errors but used -notal-check) and leads to an incorrect labelling of volumes from the -autorecon-all. My sagittal view is rotated 90 degrees clockwise on the MRI convert. The sagittal and coronal views are swapped. This appears in a tkmedit of the converted file. error codes during mri_convert are as follows: $ mri_convert '/Applications/freesurfer/subjects/001test/x-file-xx.nii.gz' '/Applications/freesurfer/subjects/001test/''orig2.mgz' mri_convert /Applications/freesurfer/subjects/001test/x-file-xx.nii.gz.nii.gz /Applications/freesurfer/subjects/001test/orig2.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/001test/HANDY_POWER_001_10_1_NIFTI.nii.gz... WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/001test/orig2.mgz guidance to fix this would be appreciated. - 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.
