Hi Bruce, I thought so. Are there any other means to accelerate this procedure (in the future)?
Best, Falk -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 21. Juli 2016 15:52 An: Falk Lüsebrink Cc: Freesurfer support list Betreff: Re: AW: AW: [Freesurfer] mri_ca_label with high resolution data Hi Falk not every part of it is accelerated, but some are cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote: > Hi Bruce, > > I'm using the current dev build: > > ProgramName: mri_ca_label ProgramArguments: --all-info > ProgramVersion: $Name: $ TimeStamp: 2016/07/21-13:42:39-GMT > BuildTimeStamp: Jul 12 2016 13:31:56 CVS: $Id: mri_ca_label.c,v 1.113 > 2016/05/13 18:02:49 fischl Exp $ User: luesebrink Machine: reco > Platform: Linux PlatformVersion: 3.16.0-4-amd64 CompilerName: GCC > CompilerVersion: 40400 > > and in the log it says to use 12 threads > > == Number of threads available to mri_ca_label for OpenMP = 12 == > > however, at least while saving the intensity scale > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > saving sequentially combined intensity scales to > aseg.auto_noCCseg.label_intensities.txt > > it doesn't seem to help. > > Best, > Falk > > ________________________________________ > Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Gesendet: Donnerstag, 21. Juli 2016 15:30 > An: Falk Lüsebrink > Cc: Freesurfer support list > Betreff: Re: AW: [Freesurfer] mri_ca_label with high resolution data > > Hi Falk > > the dev version of mri_ca_label does use openmp, so should be faster. > > cheers > Bruce > On > Thu, 21 Jul 2016, Falk Lüsebrink wrote: > >> Hi Bruce, >> >> I started the process again with openmp set to 12 using the dev build from >> 12th July. However, mri_ca_label uses only 1 thread at that point. So I >> don't assume any faster processing. >> >> Best, >> Falk >> >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce >> Fischl >> Gesendet: Dienstag, 19. Juli 2016 15:37 >> An: Freesurfer support list >> Betreff: Re: [Freesurfer] mri_ca_label with high resolution data >> >> Hi Falk >> >> I think openmp will help with this in V6, but probably not before >> Bruce >> >> On Tue, 19 >> Jul 2016, Falk Lüsebrink wrote: >> >>> >>> Hi all, >>> >>> >>> >>> I'm currently processing a 250 µm MPRAGE with a dev build from mid of May. >>> Running recon-all with default parameters ran flawlessly. Afterwards >>> I added the -hires flag to process the data without conformation. >>> However, since Saturday morning it is kind of stuck at mri_ca_label stating: >>> >>> >>> >>> saving sequentially combined intensity scales to >>> aseg.auto_noCCseg.label_intensities.txt >>> >>> >>> >>> while consuming around 30 GB of memory. I ran something similar >>> before and processing works, it's just terribly slow. Maybe this >>> particular stage is just not very efficient as it does take a few minutes >>> on 1 mm data only? >>> Would it help to add the openmp flag in that case? >>> >>> >>> >>> Best, >>> >>> Falk >>> >>> >>> >>> ---------------------------------------- >>> >>> Falk Lüsebrink, M. Sc. >>> >>> >>> >>> Otto-von-Guericke-Universität Magdeburg >>> >>> Forschungscampus STIMULATE >>> >>> http://www.forschungscampus-stimulate.de/ >>> >>> >>> >>> Universitätsplatz 2 >>> >>> 39106 Magdeburg >>> >>> >>> >>> Raum: ExFa - 4.06 >>> >>> Telefon: 0391-67-19366 >>> >>> Fax: 0391-67-19347 >>> >>> >>> >>> >>> >> >> >> > > > 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
