Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Re: [Freesurfer] System requirements
by Nick Schmansky 23 Sep '10

23 Sep '10

the memory requirements of mri_glmfit are dependent on the number of subjects given as input, the greater the subjects, the greater the ram. but generally it is not a ram hog. compiling with system specific flags might improve performance, but generally not enough to be worth the trouble. freesurfer already is compiled with maximal optimization (-O3). the GPU work is what we are targeting for substantially improved performance. n. On Thu, 2010-09-23 at 17:49 +0200, daniel geisler wrote: > Hi Nick! > > Thanks a lot for your answer. I guess that I could only benefit from > processing several subjects in parallel. Do you also have some > estimations of the resources needed by mri-glmfit? > > I notice that the source-code of freesurfer is also available. One > could suppose that compiling with system-specific optimization flags > improves performance in some way. Is it worth the trouble? > > Thank you & best wishes from Dresden, > Daniel > > On Wed, Sep 22, 2010 at 10:50 PM, Nick Schmansky > <nicks(a)nmr.mgh.harvard.edu> wrote: > the second option is best because it uses the x86 processor > (amd > opteron), which is our common distribution. the first option > uses the > Itanium processor which we dont actively support because we no > longer > have access to a build machine. > > the recon-all stream is not parallelized so you wouldnt > benefit from > multi-cores or any special parallelization hardware. runtime > on the amd > cluster would be about 25 hours per subject, and consume a > peak of about > 2.7GB of ram. each subject consumes around 400MB of hard disk > space > (budget 500MB per subject). negligible temporary hard disk > space is > used. > > n. > > On Wed, 2010-09-22 at 19:17 +0200, daniel geisler wrote: > > Dear Freesurfers! > > > > I am a new user of freesurfer and I intend to install it on > a HPC > > system. There are two different systems available (see end > of > > message). Could you please give me a hint which one is best > suited wrt > > hardware and software. > > > > In order to use these systems one also has to state some > estimations > > of the needed resources. In detail, I have to estimate: > > > > * CPU time > > * maximal number of parallel used CPUs > > * size of used RAM > > * size of permanent HDD usage > > * size of temporary HDD usage > > > > Could you share some experience how many resources are > usually used > > for the segmentation (recon-all) of a single subject? > > > > Thank you & best wishes from Dresden, > > Daniel > > > > --- > > 1.SGI Altix 4700 (Mars) > > > > * For highly parallel and memory-intensive applications > > * 2048 cores Intel Itanium II Montecito 1.6 GHz > > * 6,5 TB memory > > * One partition for interactive operation with 128 cores > > * 68 TB SAN disk storage > > * 1 PB SAN tape archive > > * SuSE Linux Enterprise Server 10, SGI ProPack 5, batch > system LSF > > * 13,1 TFlop/s peak performance > > > > 2. Linux Networx Evolocity II PC-Farm (Deimos) > > > > * For capacity computing > > * 2576 cores AMD Opteron 2,6 GHz > > * 5,4 TB memory > > * 724 nodes with 1, 2, or 4 dual-core CPUs each > > * 68 TB SAN disk storage > > * SuSE Linux Enterprise Server 10, batch system LSF > > * 13,9 TFlop/s peak performance > > > > For software specification please refer to: > > > http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/hpc/hochleis… > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > > > > > -- > > > ........................................................ > Drosselstraße 8 > 02827 Görlitz, Germany > mobile: +49 (0) 174 7932227 > e-mail: daniel.geisler(a)gmail.com > ........................................................ >

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System requirements
by daniel geisler 23 Sep '10

23 Sep '10

Dear Freesurfers! I am a new user of freesurfer and I intend to install it on a HPC system. There are two different systems available (see end of message). Could you please give me a hint which one is best suited wrt hardware and software. In order to use these systems one also has to state some estimations of the needed resources. In detail, I have to estimate: * CPU time * maximal number of parallel used CPUs * size of used RAM * size of permanent HDD usage * size of temporary HDD usage Could you share some experience how many resources are usually used for the segmentation (recon-all) of a single subject? Thank you & best wishes from Dresden, Daniel --- 1.SGI Altix 4700 (Mars) * For highly parallel and memory-intensive applications * 2048 cores Intel Itanium II Montecito 1.6 GHz * 6,5 TB memory * One partition for interactive operation with 128 cores * 68 TB SAN disk storage * 1 PB SAN tape archive * SuSE Linux Enterprise Server 10, SGI ProPack 5, batch system LSF * 13,1 TFlop/s peak performance 2. Linux Networx Evolocity II PC-Farm (Deimos) * For capacity computing * 2576 cores AMD Opteron 2,6 GHz * 5,4 TB memory * 724 nodes with 1, 2, or 4 dual-core CPUs each * 68 TB SAN disk storage * SuSE Linux Enterprise Server 10, batch system LSF * 13,9 TFlop/s peak performance For software specification please refer to: http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/hpc/hochleis…

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-legacy
by Juranek, Jenifer 23 Sep '10

23 Sep '10

I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't look like a legacy analysis (see below). [jjuranek@localhost subjects]$ recon-all -legacy -s SB_057_H21001 ERROR: you have specified -legacy, but this does not look like a legacy analysis. My recon-all.log file for this subjid reports the following build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 How do I convince FSv5.0.0 that I am feeding it legacy data from FSv4.0.5? Have I skipped too many versions to use this -legacy flag? Many thanks, Jenifer

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Question about 'mri_surf2surf' and vertex index sorting
by orangekic 23 Sep '10

23 Sep '10

Hi, Could someone tell me the way how 'mri_surf2surf' resample one subject onto fsaverage? How can I know the specific point comes from in the native space? for example: [subject A] vertex index 1, (x, y, z) ---------<mri_surf2surf>--------> [subject A in subject B coordinate] vertex index ??, (x', y', z') I'm using 'mris_convert' to convert the thickness file to ascii format, include vertex index, (x, y, z), and thickness information. I'm wondering that what's the rule to sort the vertex index? And, how can I know the relationship between vertex index and the label other than in tksurfer or tkmedit? Best

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Re: [Freesurfer] iPhone and IPad FreeSurfer based atlas
by Pedro Paulo de Magalhães Oliveira Junior 22 Sep '10

22 Sep '10

http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8 The download link for United States -- via iPhone iOS4 Em 22/09/2010, às 20:50, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> escreveu: > > On Wed, 2010-09-22 at 19:17 -0300, Pedro Paulo de Magalhães Oliveira > Junior wrote: >> More news on the free brain atlas app for IPhone using FreeSurfer >> aseg. >> >> Today we have another major upgrade: >> >> >> - Pinch and Zoom >> - Many papers for Reading >> - Improved documentation of FreeSurfer >> >> http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 >> >> Suggestions for the upcoming version are welcome. >> >> Cheers >> >> Pedro Paulo Jr. >> >> -- via iPhone iOS4 >> --------------------------------------------------------------------- >> Pedro Paulo de Magalhães Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> -- www.netfilter.com.br >> -- For mobile: http://www.netfilter.com.br/mobile >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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.

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iPhone and IPad FreeSurfer based atlas
by Pedro Paulo de Magalhães Oliveira Junior 22 Sep '10

22 Sep '10

More news on the free brain atlas app for IPhone using FreeSurfer aseg. Today we have another major upgrade: - Pinch and Zoom - Many papers for Reading - Improved documentation of FreeSurfer http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version are welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4 --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

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RAM question
by O'Shea, Colin (NIH/NIMH) [V] 22 Sep '10

22 Sep '10

I realize that FreeSurfer requires at least 4 GB RAM, and I'm in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)? Thanks, Colin

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GLM question
by Gabriel Go.Es. 22 Sep '10

22 Sep '10

Hello everybody I'm wondering about how to perform an FDR correction using the glmfit on FS?, I mean using command line if there is one; And Could it be applied the same sentence to correct at cortex level and clusters label, or need some special arguments on the command line for any of them? Thanks in advance Gabriel

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nframes file parameter...
by Gonzalo Rojas Costa 22 Sep '10

22 Sep '10

Hi: What it means the "nframes" parameter ?... Which is the difference between a 001 mgz file that has "dimensions: 256 x 256 x 176" and another that has "dimensions: 256 x 256 x 176 x 2" ?... Sincerely, Gonzalo Rojas Costa

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changing f.nii nframes
by raij＠nmr.mgh.harvard.edu 22 Sep '10

22 Sep '10

Dear Free Surfers, I am analyzing fMRI time series that were reconstructed offline (GRAPPA data that needed some artifact corrections, long story). Unfortunately, the offline reconstructed f.nii do not include proper header info. I think I was able to set the orientations correctly using mri_convert, but now FSFAST preprocessing (specifically, mc-sess) fails because the headers say that the number of TRs (number of full volume acquisitions) in the measurement is 1, whereas in fact the correct value is 316. I could not find a tool that could change the "nframes" value (mri_convert can adjust many other things but not this one it seems). Any suggestions? Bests, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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