[Freesurfer] mri_ca_label with high resolution data
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 ___ 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] 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 ___ 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] mri_ca_label with high resolution data
Hi Bruce, thanks for the quick reply. I'll try it out once I have a bit of memory available and let you know if it helped. 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 > > > > > ___ 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] mri_ca_label with high resolution data
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 > > > > > ___ 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] 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 ___ 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] mri_ca_label with high resolution data
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
Re: [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 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] mri_ca_label with high resolution data
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
Re: [Freesurfer] mri_ca_label with high resolution data
Hi Falk yes, it's an active area of devlopment for us cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote: 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 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] mri_ca_label with high resolution data
Hi Bruce, thanks. Keep up the fantastic work! Best, Falk -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 21. Juli 2016 16:44 An: Falk Lüsebrink Cc: Freesurfer support list Betreff: Re: AW: AW: AW: [Freesurfer] mri_ca_label with high resolution data Hi Falk yes, it's an active area of devlopment for us cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote: > 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
