Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference
by Hemant Bokil 25 Oct '11

25 Oct '11

Hi all, Here are the details of my freesurfer and linux installations FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS Linux release 6.0 (Final) Kernel info: Linux 2.6.32-71.29.1.el6.x86_64 x86_64 I successfully ran autorecon2 without gpu on several datasets that we have. However, when I try to use the GPU, I get the following error message: CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference The calling sequence and all on-screen messages are listed at the end of this email. A similar error was reported a year ago by a different user ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-August/015528.h…) so I am hoping there is a simple fix. Thanks in advance, Hemant recon-all -subjid 203 -use-gpu -autorecon2 Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0.2.1221 Driver : 4.10 Runtime : 3.20 Acquiring CUDA device Using default device CUDA device: Quadro FX 4600 stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 285.05.09 Fri Sep 23 17:31:57 PDT 2011 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/hemant/FreeSurferSubjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r--. 1 hemant hemant 226454 Oct 24 15:05 /home/hemant/FreeSurferSubjects/203/scripts/recon-all.log Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux #------------------------------------- #@# EM Registration Mon Oct 24 15:05:52 EDT 2011 /home/hemant/FreeSurferSubjects/203/mri mri_em_register_cuda -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0.2.1221 Driver : 4.10 Runtime : 3.20 Acquiring CUDA device Using default device CUDA device: Quadro FX 4600 aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference. register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 Abort (core dumped) Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 203 exited with ERRORS at Mon Oct 24 15:06:11 EDT 2011

2 4

hippocampal subfields
by Lugar, Heather 25 Oct '11

25 Oct '11

If I were to run the hippocampal subfields command on data that had been previously processed using Freesurfer 5.0 (rather than 5.1), would the results be valid? Thanks, Heather

1 0

Fwd: BEM surface generation questions
by Dan G Wakeman 25 Oct '11

25 Oct '11

Hi, I have a couple of questions about the two different ways to generate BEM surfaces available in FreeSurfer. I have done a comparison of the techniques available in mri_watershed -surf mri_make_bem_surfaces (Version 4.3.0) with another algorithm (which I know the algorithm) I have received a request from reviewers to briefly describe how each of the first two techniques develops the surfaces. I have read all of the Ségonne 2004 paper several times and while I believe I can explain how the "brain"/"inner skull" surface is generated. I cannot figure out how the other two surfaces are generated: "outer skull" and "outer skin" surfaces. Additionally, I cannot find any information about mri_make_bem_surfaces either on the wiki or in the email archives (I realize this software may be kept in as a courtesy to the MEG users: my tests suggest this is very useful). Is there anyone who can provide even a brief description of how this tool generates the surfaces? Thank You, Dan

1 0

Diffusion tensor estimation method
by Ed Gronenschild 25 Oct '11

25 Oct '11

Hi, There are various methods to estimate the diffusion tensor, like linear-least squares, non-linear least-squares, German-McClure M-estimator..... I would like to know which method is used by FreeSurfer in the dt_recon command? Cheers, Ed

2 1

Re: [Freesurfer] white matter volume in a ROI
by Douglas N Greve 25 Oct '11

25 Oct '11

Yes, I see what you mean. mri_aparc2aseg is hard coded to accept both hemis. The easiest way around it is just to create a dummy label for the right hemisphere. doug dolphinede(a)aol.com wrote: > Hi Doug, > > thanks a lot your advice. > > I created an annnotation of my ROI-label as called > lh.cluster1.labe.label with the command line: > > /mris_label2annot --s ZPN20 --h lh --ctab > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a > myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh > > This works fine. After that i have used your commmand in this way: > > m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/ > > and i get the following error, which is cause that i have no > lh.cluster1.labe.label in the right hemisphere: > > /Loading lh annotations from > /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot > reading colortable from annotation file... > colortable with 36 entries read (originally > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab) > > Reading rh white surface > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white > > Reading rh pial surface > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial > > Loading rh annotations from > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > could not read annot file > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > No such file or directory > ERROR: MRISreadAnnotation() failed > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/ > > The question i have is if all these steps are right and/if i have to > do some more steps to get white matter volume of my annotation and > where i can find it? > > Excuse my numerous questions but I am just a freesurfer-beginner... > > Best regards > > Daniel > > > > > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: dolphinede <dolphinede(a)aol.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > Verschickt: Mo, 24 Okt 2011 10:04 pm > Betreff: Re: [Freesurfer] white matter volume in a ROI > > It will be more involved than that. You will need to create an > annotation that contains your label (maybe in addition to other labels), > then uses mri_aparc2aseg with the --labelwm option, something like > > mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot > > doug > > dolphinede(a)aol.com <mailto:dolphinede@aol.com> wrote: > > Hi Doug, > > > > thanks a lot for your answer. > > > > So i understand you right that i can get "exact" knowledge about the > > thickness, grey matter volume and pial surface area in my ROI, but in > > case of "the" ROI white matter volume, i have to look to which > > cortical label my ROI counts and then I use the wmparc.files for this > > label? > > > > Best regards > > > > Daniel Klein > > > > > > > > > > > > > > > > > > > > -----Ursprüngliche Mitteilung----- > > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > An: dolphinede <dolphinede(a)aol.com <mailto:dolphinede@aol.com>> > > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Verschickt: Mo, 24 Okt 2011 4:48 pm > > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > > For GM area and volume, you can use mris_anatomical_stats. See the > > recent thread on how. For the WM volume, how would you define the WM > > volume that corresponds to you label? We have a routine that parcellates > > WM based on closest proximity to a cortical label. > > doug > > > > dolphinede(a)aol.com <mailto:dolphinede@aol.com> wrote: > > > Dear FreeSurfer experts, > > > > > > i have created a ROI in qdec , where i have found a significant > > > correlation between lgi and age. > > > > > > I mapped this ROI to all subjects. > > > > > > I am interested to compare in this ROI the pial-surface area, the grey > > > matter volume and if possible the white matter volume for this > > > specific region and i am not sure how to do this? > > > > > > Best regards > > > > > > Daniel Klein > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.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/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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

Re: [Freesurfer] roi analysis from label or annotation
by Douglas N Greve 25 Oct '11

25 Oct '11

Did you try passing --olab a full path? Knut J Bjuland wrote: > Hi > > I use mri_surfcluster -olab --subject fsaverage --in sig.mgh --hemi ?h > to produce label for the areas indicated by mri_glmfit. Then I use > label and mean follow by the python script. > > > cheers > Knut J > > I use > > > Date: Mon, 24 Oct 2011 10:43:02 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: knutjbj(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] roi analysis from label or annotation > > > > It's very hard to tell what you are doing without a command-line. > > Generally, you can pass the full path of a label to surfcluster to make > > it save it in a particular location. > > doug > > > > Knut J Bjuland wrote: > > > I am working on roi analysis. I have made a label using > mri_surdcluster and used mri_label2label to > > > copy the label from fsaverage to each individual subject. The next > step would be to use > > > mris_anatomical_stats to calculate stats for each subject. I used > a Python to merge the txt file from > > > mris_anatomical_stats. > > > > > > Is it possible to force mri_surfcluster to save the label another > dir than fsaverage? > > > Can I use convert roi label to annotation and then use aparc2stats > > > or similar command to get group statics? > > > > > > > > > Cheers > > > Knut J > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)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 > > > > > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

Question on mris_pmake
by Jungwon Ryu 25 Oct '11

25 Oct '11

Hi, I'm trying to get distances on a cortical surface between sets of voxels in visual areas and I have two questions; 1) I have the following error message so often; === System error: Address already in use Fatal error encountered. SSocket `Unnamed SSocket_UDP_receive' (id: 0) Current function: c_SSocket_UDP_receive::c_SSocket_UDP_receive Problem binding to socket 1701 Error returned from system: Address already in use Throwing exception to (this) with code 1 terminate called after throwing an instance of 'c_SSocket*' runSh_Ori_1_02_01.sh: line 5789: 93334 Abort trap mris_pmake --subject JR20110819 --hemi rh --surface0 white --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:907,endVertex:731 >> result_Ori_1_02_01.txt === I have around 10,000 voxel pairs to run mris_pmake( ) command. Since I have to call mris_pmake( ) so many times (one pair by one pair), I splitted the whole list of voxel pairs into four script files, containing many mris_pmake commands with 2,500 voxel pairs as arguments, then I ran scripts with four terminal windows saparately to parallelize the processing. All script files are located in the same diretory. Then I had the message as above. What might be the problem? (It seems as if multiple terminal instances share the socket port number) 2) How can I get interhemispheric distances between visual areas across hemispheres? Ryu PhD student Department of Brain and Cognitive Sciences, Seoul National University, Korea

1 0

Re: [Freesurfer] mris_anatomical stats different thickness files
by Douglas N Greve 24 Oct '11

24 Oct '11

no, that would be 15 "smooth steps". If you want to smooth by 15mm, then use mris_fwhm. doug krista kelly wrote: > Would the following code give me data smoothed with 15 fwhm kernel? > > mris_anatomical_stats -l lh.v1.label -t lh.thickness -nsmooth 15 -b -f > BV01/stats/lh.v1_pial.stats BV01 lh pial > > > Thanks! > > > On Mon, Oct 24, 2011 at 10:40 AM, krista kelly > <krista.kelly16(a)gmail.com <mailto:krista.kelly16@gmail.com>> wrote: > > Thanks for clearing this up! It makes a lot more sense now. > > > On Mon, Oct 24, 2011 at 10:35 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > krista kelly wrote: > > I'm looking at both cortical thickness and surface area > differences between two groups. I've been using > mris_anatomical_stats to retrieve values but had a few > questions: > > 1) Do I need to do separate mris_anatomical_stats using > different thickness files (bolded below) to get cortical > thickness and surface area measures. For example: > > cortical thickness - mris_anatomical_stats -l lh.v1.label > -t *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh > surface area - mris_anatomical_stats -l lh.v1.label -t > *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh > > > Or, since the output files include all of these measures, > is it fine to just run one of the two? > > Just run the first one. > > > 2) The output files for both analyses run above (with > different thickness files) have identical values for > everything except for tray matter volume. Using > lh.thickness file - grayvol = 8082; using lh.area file - > grayvol = 4029. Can anyone clarify why this happens? > > It computes the gray matter volume by thickness*area. If you > pass it "area" as the "thickness", then you are probably > getting area*area. Though I'm surprised that the "thickness" > values are correct. > > > 3) The default surface area values are for the white > matter surface. How do I run mri_anatomical_stats to get > the pial surface? I've tried mris_anatomical_stats -l > lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats > BV01 lh but I get identical values for everything (except > grayvol). > > Try adding "pial" to the end of the command line (and use > lh.thickness) > doug > > > Thanks! > Krista > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: > 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.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/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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

Re: [Freesurfer] white matter volume in a ROI
by Douglas N Greve 24 Oct '11

24 Oct '11

It will be more involved than that. You will need to create an annotation that contains your label (maybe in addition to other labels), then uses mri_aparc2aseg with the --labelwm option, something like mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot doug dolphinede(a)aol.com wrote: > Hi Doug, > > thanks a lot for your answer. > > So i understand you right that i can get "exact" knowledge about the > thickness, grey matter volume and pial surface area in my ROI, but in > case of "the" ROI white matter volume, i have to look to which > cortical label my ROI counts and then I use the wmparc.files for this > label? > > Best regards > > Daniel Klein > > > > > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: dolphinede <dolphinede(a)aol.com> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Verschickt: Mo, 24 Okt 2011 4:48 pm > Betreff: Re: [Freesurfer] white matter volume in a ROI > > For GM area and volume, you can use mris_anatomical_stats. See the > recent thread on how. For the WM volume, how would you define the WM > volume that corresponds to you label? We have a routine that parcellates > WM based on closest proximity to a cortical label. > doug > > dolphinede(a)aol.com wrote: > > Dear FreeSurfer experts, > > > > i have created a ROI in qdec , where i have found a significant > > correlation between lgi and age. > > > > I mapped this ROI to all subjects. > > > > I am interested to compare in this ROI the pial-surface area, the grey > > matter volume and if possible the white matter volume for this > > specific region and i am not sure how to do this? > > > > Best regards > > > > Daniel Klein > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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 > > > > 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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

Re: [Freesurfer] implementation on Neurodebian
by Cartik Sharma 24 Oct '11

24 Oct '11

Hi Knut, Good to know we can speed things up with CUDA. I have a multicore CPU and was wondering if there is a parallelized version of Freesurfer on the CPU. Thanks for the speedup! Best regards, Cartik On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote: Hi Cartik You use -use-gpu to offload rendering to the GPU using cuda. Knut J > From: Cartik.Sharma(a)childmind.org<mailto:Cartik.Sharma@childmind.org> > To: knutjbj(a)hotmail.com<mailto:knutjbj@hotmail.com> > Subject: Re: [Freesurfer] implementation on Neurodebian > Date: Thu, 20 Oct 2011 15:48:10 +0000 > > Hi Knut: > > Cool..is this speeding up things by rendering on the GPU. > Is there a way to offload computation to the GPU. > > Best regards, > Cartik > > On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote: > > > Hi Cartik > > > > If you enable cuda with -use-gpu the recon-all will run faster. > > > > Knut J > > > > Den 17.10.2011 16:41, skrev Cartik Sharma: > >> Dear Freesurfer developer(s), > >> > >> Is there a way to get Freesurfer run faster on Neurodebian. While the package produces > >> some truly out of the world segmentations and labels for the cortical surface, it seems > >> to take time. > >> > >> For eg: > >> Defect correction and retesellation takes an hour, other steps take longer..I'm not sure if > >> it's the original dataset, the OS platform (i.e Virtual Machine, Neurodebian) or original > >> computational engine itself. > >> > >> Would be happy in efforts and hints to make this run faster. > >> > >> Best regards, > >> Cartik Sharma > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu<mailto: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. > >> > >> > >> > > >

3 4

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer