Re: [Freesurfer] ftp server down??
Will do. Gen On Tue, Aug 24, 2010 at 8:10 PM, Paul Raines wrote: > Try back in 24 hours. Our storage servers are down right now > > On Tue, 24 Aug 2010, Gennan Chen wrote: > >> No. Still down. >> >> Gen >> >> >> >> On Tue, Aug 24, 2010 at 6:30 PM, Bruce Fischl >> wrote: >>> >>> Hi Gen, >>> >>> yes, we've had some local hardware issues. Is it up now? >>> >>> cheers >>> Bruce >>> On Tue, 24 Aug 2010, Gennan Chen wrote: >>> Hi! I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. Is it down? Gen ___ 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 >> >> >> > > -- > --- > Paul Raines email: raines at nmr.mgh.harvard.edu > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > 149 (2301) 13th Street Charlestown, MA 02129 USA > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ftp server down??
Try back in 24 hours. Our storage servers are down right now On Tue, 24 Aug 2010, Gennan Chen wrote: > No. Still down. > > Gen > > > > On Tue, Aug 24, 2010 at 6:30 PM, Bruce Fischl > wrote: >> Hi Gen, >> >> yes, we've had some local hardware issues. Is it up now? >> >> cheers >> Bruce >> On Tue, 24 Aug 2010, Gennan Chen wrote: >> >>> Hi! >>> >>> I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. >>> Is it down? >>> >>> Gen >>> ___ >>> 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 > > > -- --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ftp server down??
No. Still down. Gen On Tue, Aug 24, 2010 at 6:30 PM, Bruce Fischl wrote: > Hi Gen, > > yes, we've had some local hardware issues. Is it up now? > > cheers > Bruce > On Tue, 24 Aug 2010, Gennan Chen wrote: > >> Hi! >> >> I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. >> Is it down? >> >> Gen >> ___ >> 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
Re: [Freesurfer] ftp server down??
Hi Gen, yes, we've had some local hardware issues. Is it up now? cheers Bruce On Tue, 24 Aug 2010, Gennan Chen wrote: > Hi! > > I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. > Is it down? > > Gen > ___ > 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] How to add volume on pial surface in manual editting the trouble shootings
Hi Jin you have to identify the problem. Is it that the white matter surface is incorrect so the pial doesn't get out far enough? Are the intensites in the wm and gm darker in that region? Is there a gm leson? If you upload the dataset we'll take a look cheers Bruce On Tue, 24 Aug 2010, [GB2312] Àîèª wrote: Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin ___ 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] ftp server down??
Hi! I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. Is it down? Gen ___ 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] tkmedit and intensity normalisation
I don't know about the 1st question, but on the 2nd question, you do not have to rerun recon-all twice if you fix both of them at the same time. doug Ali Radaideh wrote: > > Dear FreeSurfer experts, > > I have two question for you please, > > First, I started recently to get the following message when I try to > load the tkmedit > > GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported > by display: IP address > > And sometimes > > tkmedit.bin: xcb_io.c:452: _XRead: Assertion `dpy->xcb->reply_data != > 0' failed. aborted > > > > > > Second, I have some images that have both intensity normalisation and > Geometric distortion due to MS lesions. I followed the tutorial on how > to fix these problems. My question is that, I don't want to re-run > freesurfer twice (when I fix the intensity normalisation and one when > I edit the white matter). Is there any command line I can use after > saving changes to do both?. > > > > > Many thanks in advance > > Ali > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please send it back to me, and immediately delete > it. Please do not use, copy or disclose the information contained in > this message or in any attachment. Any views or opinions expressed by > the author of this email do not necessarily reflect the views of the > University of Nottingham. > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK legislation. > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.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] tkmedit and intensity normalisation
Dear FreeSurfer experts, I have two question for you please, First, I started recently to get the following message when I try to load the tkmedit GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: IP address And sometimes tkmedit.bin: xcb_io.c:452: _XRead: Assertion `dpy->xcb->reply_data != 0' failed. aborted Second, I have some images that have both intensity normalisation and Geometric distortion due to MS lesions. I followed the tutorial on how to fix these problems. My question is that, I don't want to re-run freesurfer twice (when I fix the intensity normalisation and one when I edit the white matter). Is there any command line I can use after saving changes to do both?. Many thanks in advance Ali This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.___ 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] How to add volume on pial surface in manual editting the trouble shootings
we don't actually have a way to edit the pial surface. Usually, the problem you describe is an intensity normalization problem, so you might want to put some control points near the place where the pial surface is in error. Be careful putting in the control points. You want to make sure that they are truly in white matter. Look at the control points/intensity normalization tutorial on the wiki. doug ?? wrote: > Dear freesurferers > I have faced a problem in editing pial surface in trouble shootings. > Since the page > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has > showed how to delete volume which is really useful, however, we faced > another problem, that is how to add volume. I selected the edit voxels > tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and > used the middle button on the mouse, but did not see any change on the > main volume. > The skull strip is fine, so I need not edit the skull strip, but some > brain tissue was not included by the red line (represent the pial > surface). > Could anybody tell me how to add volume on pial surface in manual > editting the trouble shootings? > Thanks in advance! > Jin > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.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] How to add volume on pial surface in manual editting the trouble shootings
Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin ___ 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] how to expand the disk size if I use VirtualBoxFS45
Hi, there, Thanks a lot for your help, now I have attached the new vdi to the old vid, but I still can not access the new space after I restart the old vdi. I searched online, it looks like I'd use some software to clone the old vdi to the new vdi, then set the new vdi as the primary master, is it correct? Thanks! Guang From: p...@netfilter.com.br Date: Mon, 23 Aug 2010 16:50:18 -0300 Subject: Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45 To: freesurfer...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu you can use the Virtual Disk Manager GUI from Virtual Box's File menu - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Mon, Aug 23, 2010 at 16:36, Guang Zeng wrote: Thanks a lot, could you give me more details? Thanks! Guang > From: p...@netfilter.com.br > Date: Sun, 22 Aug 2010 21:24:02 -0300 > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45 > > You can create another virtual disk and attach to your virtual machine > > -- via iPhone iOS4 > > Em 22/08/2010, às 16:16, Guang Zeng escreveu: > > > Hi, there, > > > > I am using VirtualBoxFS45 now, everything is fine. > > But I find that after I load the FSVirtualBox.vdi, the default storage > > space is about 8GB. > > > > I'd like to use FreeSurfer to run multiple subjects (about 100), and then > > do group analysis using QDEC, however the > > 8GB disk space limit will be a big problem. > > > > Anyone know how to expand (or change) the default 8GB disk space in > > VirtualBox? > > > > Thanks a lot! > > Guang > > ___ > > 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 ___ 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...
no sure about that error, but clearly we need to look at that devicemanagement.cu code as it seems to be the gate keeper to getting anything running. we'll see if we can get that code to produce some useful error message and post a new _cuda tarball. n. On Tue, 2010-08-24 at 11:48 -0400, Gonzalo Rojas Costa wrote: > Hi: > > I installed the latest NVIDIA driver (256.44) in my DELL Precision T3500 > (Quadro FX-580 graphic board, Ubuntu 9.04)... Then I installed CUDA Toolit > 3.1 (for Ubuntu 9.10)... Then, I restart my computer... I tried to process a > study with the freesurfer command: > > "recon-all -autorecon1 -s ingrid -use-gpu", > > but I got the error: > > "/home/gonzalorojas/freesurfer/subjects/ingrid/mri > > mri_em_register_cuda -skull nu.mgz > /home/gonzalorojas/freesurfer/average/RB_all_withskull_2008-03-26.gca > transforms/talairach_with_skull.lta > > Acquiring CUDA device > Using default device > CUDA Error in file 'devicemanagement.cu' on line 46 : unspecified driver > error. > Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 > GNU/Linux > > recon-all -s ingrid exited with ERRORS at Tue Aug 24 11:46:20 CLT 2010" > > How can I find a solution to that problem ?... > > Sincerely, > > > Gonzalo Rojas Costa > > > ___ > 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] Notes on CUDA Acceleration
since we'll be providing updates to these _cuda binaries (in the form of the fscudabins_linuc_centos4*.tgz tarballs), i'll make sure they are built with the 1.1 architecture in our stable branch. i'm thinking our plan will be to conform to the 1.1 architecture for the near term stable release _cuda binaries, with internal development targeted at the fermi-class cards. at some point (probably not till next year), we'll make the decision as to which lowest architecture to support, or perhaps we can figure out a way to conditionally compile the code to support multiple architectures. it will be a give-and-take with the cuda user base and us, as we figure out what cards people have, and what architecture elements are essential to make cuda/freesurfer worthwhile. n. On Tue, 2010-08-24 at 10:08 -0400, Richard G. Edgar wrote: > On Tue, 2010-08-24 at 10:55 -0300, Pedro Paulo de Magalhães Oliveira > Junior wrote: > > > Just to clarify one point: when you mentioned CUDA architecture 1.3 I > > think you did mean Cuda Computing Capability 1.3 > > Indeed - it's the -arch flag to the compiler, hence I got mixed up. > > We haven't tested this, but I think that any card with compute > capability 1.1 will work with the released code, provided the -arch flag > is changed. However, I don't have a card to check this, and doing so is > not a priority. > > Regards, > > Richard > > ___ > 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.
[Freesurfer] CUDA error...
Hi: I installed the latest NVIDIA driver (256.44) in my DELL Precision T3500 (Quadro FX-580 graphic board, Ubuntu 9.04)... Then I installed CUDA Toolit 3.1 (for Ubuntu 9.10)... Then, I restart my computer... I tried to process a study with the freesurfer command: "recon-all -autorecon1 -s ingrid -use-gpu", but I got the error: "/home/gonzalorojas/freesurfer/subjects/ingrid/mri mri_em_register_cuda -skull nu.mgz /home/gonzalorojas/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : unspecified driver error. Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all -s ingrid exited with ERRORS at Tue Aug 24 11:46:20 CLT 2010" How can I find a solution to that problem ?... Sincerely, Gonzalo Rojas Costa ___ 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] Notes on CUDA Acceleration
On Tue, 2010-08-24 at 10:55 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote: > Just to clarify one point: when you mentioned CUDA architecture 1.3 I > think you did mean Cuda Computing Capability 1.3 Indeed - it's the -arch flag to the compiler, hence I got mixed up. We haven't tested this, but I think that any card with compute capability 1.1 will work with the released code, provided the -arch flag is changed. However, I don't have a card to check this, and doing so is not a priority. Regards, 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] Notes on CUDA Acceleration
Greetings, I've been asked to provide some extra information about GPU support in Freesurfer (being the one guilty of mri_em_register_cuda...). Firstly, there are no immediate plans for OpenCL support. It would be very nice to have - with ATI, NVIDIA _and_ x86 multicore backends. However, it's far less mature than CUDA. The good news is that the really 'hard' bit is restructuring the algorithms to fit well on a GPU. The syntax of CUDA and OpenCL is very similar (strange that), but OpenCL is more verbose. As for cards. for what is in the current release, any GeForce GTX-200 series or Tesla 10 series (i.e. C1060 and S1070) card should work (I don't know the Quadro model numbers - CUDA architecture 1.3 is the key feature). I think that everything should actually work on somewhat older cards, but the compile flags will have to be tweaked. So long as that threshold is reached, the only issue is the amount of RAM needed. Currently, I expect that any card with at least 1 GiB of RAM will have plenty, and the threshold for mri_em_register_cuda will be much lower than that. Going forward, I would strongly recommend purchasing 'Fermi' class cards. These are the GTX 400 series, and Tesla 20 series. The new architecture lifts some hardware limits on GPU kernels which are crippling for portions of mri_ca_register. With a more accelerated mri_ca_register, RAM limits may also come into play, until I can come up with a suitably cunning GPU implementation of the Gaussian Classifier Array (right now, I'm going to burn around 2 GiB on a single GCA, to make implementation simple). However, I have bigger fish to fry first. One final thing: Nick and I found last week that the accelerated mri_em_register_cuda doesn't seem to work prior to skull stripping. I'm going to work on this this week, but if you want to continue using the GPU accelerated binary, you'll have to turn off the FAST_TRANSLATION and FAST_TRANSFORM flags in mri_em_register.c, and recompile. This will increase the runtime to around 4 minutes on ernie, but will give results identical to the CPU code. I hope this is helpful, 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.
Re: [Freesurfer] From mgz to m3z
Hi Soon, sorry, but I don't think we have any binaries that will do this specifically. Bruce On Tue, 24 Aug 2010, Soon Hock Wei wrote: Dear All: Can any kind soul please enlighten me on this: If let's say I am given these mgz files: transforms/talairach.m3z.inv.x.mgz transforms/talairach.m3z.inv.y.mgz transforms/talairach.m3z.inv.z.mgz (the output from -careginv) Is it possible for me to recover the input m3z file? If possible, how? Thanks! Regards, Soon ___ 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] From mgz to m3z
Dear All: Can any kind soul please enlighten me on this: If let's say I am given these mgz files: transforms/talairach.m3z.inv.x.mgz transforms/talairach.m3z.inv.y.mgz transforms/talairach.m3z.inv.z.mgz (the output from -careginv) Is it possible for me to recover the input m3z file? If possible, how? Thanks! Regards, Soon ___ 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 vs. ATI Stream / OpenCL
Hi Nick, We are planning to buy a GTX 460 1G card because of the cuda support of Freesurfer. It seems the most reasonable buy for CUDA device, 336 Core, 1350MHZ shader, and around 100 $ cheaper than the 285GTX. Does this card has double precision support? And what is you guess (time) about the stable CUDA support for let's say 50-70% of freesurfer stream? Thanx, Gergo 2010/8/23 Nick Schmansky > we're still trying to find the 'lowest common denominator' card to > support, as clearly have more memory and double precision support allows > more efficiency options in development. currently we target the Quadro > FX4800, which is about the same as the GTX 285, as the LCD card, but we > test and develop on a C1060 and C2050 as well. a tesla card is useful > if you plan to process multiple subjects on one processor (assuming you > have a multicpu with tons of memory) and you want to have a gpu per > processor. otherwise, for our current gpu stream, a tesla is overkill. > > n. > > > On Mon, 2010-08-23 at 00:04 +0200, Georg Homola wrote: > > Hi Nick (and others), > > > > do you already have positive experience with ATI cards, too? We think > about > > buying a new workstation with lots of GPU power so it would be great help > to > > know what really pays off: GeForce GTX 480 or ATI Radeon HD 5870? Or > should > > we go for Nvidia Tesla? What kind of tech specs are important here? > Double > > or single precision floating point performance, number of cores, amount > of > > memory... > > > > Thanks and cheers, > > Georg > > > > > > ___ > > 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. > > -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.o...@gmail.com ___ 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.
