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
