Dear Bruce and FS experts,I am running recon-all using the longitudinal stream. I have a question regarding the specific command line for recon-all using the -openmp flag and regarding the organizing directory of longitudinal data. I am using FS version 5.3 CentOS 6 and in a linux work station with two processors with 4 cores (8 cores total).As far as I understand I can use the openmp 8 flag. But I just wanted to confirm the exact command line would be [recon -all -s -openmp 8] ?Also, do I need to include this flag for importing the files: [e.g. recon-all -i ... -s -openmp 8 ...] One last query, is there any command lines for organizing the subjects in terms of time point 1 and time point 2 for each subject?Thank you,Pablo > > Date: Tue, 26 Nov 2013 16:41:31 -0500 > > From: fis...@nmr.mgh.harvard.edu > > To: pablon...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > Hi Pablo > > > > it also depends on how much ram it has. You should be able to run 1 > > significantly faster using the -openmp 8 flag to recon-all, or 8 (if you > > have enough ram, probably at least 32G) > > > > cheers > > Bruce > > > > On Tue, 26 Nov 2013, pablo najt > > wrote: > > > > > Dear Bruce,Last week I emailed with the question of how many recon -all > > > separate subjects I could run in parallel with the FS version 5.3 for Cent > > os > > > 6. You answered that this depends on how many cores my machine has. > > > I just found out that our workstation has two processors with 4 cores each > > > (8 cores in total). > > > Would you be able to tell me how many subjects could I run in parallel wit > > h > > > our workstation? > > > Thank you for your support, > > > Pablo > > > > > > Date: Thu, 21 Nov 2013 10:47:34 -0500 > > > From: fis...@nmr.mgh.harvard.edu > > > To: pablon...@hotmail.com > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6 > > > > > > Hi Pablo > > > > > > it depends on how many cores you have > > > > > > Bruce > > > On Thu, 21 Nov 2013, pablo najt wrote: > > > > > > > Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I > > a > > > m > > > > wondering up to how many recon -all for separate subjects I can run in > > > > parallel. With the version of Snow Leopard 32b I was running two at a ti > > me > > > > and it took around 20 hours. Would I be able to run 6 subjects in parall > > el > > > ? > > > > If so would this process still efficient or there is an optimum number? > > > > Thank you, > > > > Pablo > > > > > > > > > Date: Wed, 20 Nov 2013 13:11:15 -0500 > > > > > From: zkauf...@nmr.mgh.harvard.edu > > > > > To: gariko...@gmail.com > > > > > CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and > > > > CentOS 6 > > > > > > > > > > I have to agree with Gari, I see no reason for you to not use the > > > > > CentOS6 build. > > > > > > > > > > -Zeke > > > > > > > > > > On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: > > > > > > I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in a > > ny > > > > > > reason to not use this version in your CentOS 6, if you have some ot > > he > > > r > > > > > > requirements maybe Nick or Zeke could help you better, I am just an > > us > > > er > > > > :) > > > > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablon...@hotmail.com > > > > > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > > > > > > > Dear Gari, > > > > > > Thank you for the advice. One additional question. > > > > > > Considering that I will start from scratch the processing in the > > > > > > CentOS 6, which would be the recommended FS version for CentOS 6? > > > > > > Thanks, > > > > > > Pablo > > > > > > > > > > > > -------------------------------------------------------------------- > > -- > > > -- > > > > > > From: gariko...@gmail.com <mailto:gariko...@gmail.com> > > > > > > Date: Wed, 20 Nov 2013 18:23:40 +0100 > > > > > > To: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > > Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > > and CentOS 6 > > > > > > > > > > > > > > > > > > Hi Pablo, > > > > > > you shouldn't mix different OS-s or software version in the same > > > > > > study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., > > > > > > Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The > > > > > > effects of FreeSurfer version, workstation type, and Macintosh > > > > > > operating system version on anatomical volume and cortical thickness > > > > > > measurements. /PloS one/, /7/(6), e38234. > > > > > > doi:10.1371/journal.pone.0038234). > > > > > > > > > > > > for the CentOS 6 you should install CentOS 6 (if you want version 4 > > > > > > it works too). > > > > > > regards! > > > > > > Gari > > > > > > > > > > > > > > > > > > On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablon...@hotmail.com > > > > > > <mailto:pablon...@hotmail.com>> wrote: > > > > > > > > > > > > Dear FS experts, > > > > > > I am forwarding my question (please see below), in case it got > > > > > > lost among the intense flow of messages. > > > > > > Thank you for your consideration. > > > > > > Pablo > > > > > > > > > > > > -------------------------------------------------------------------- > > -- > > > -- > > > > > > From: pablon...@hotmail.com <mailto:pablon...@hotmail.com> > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > > > Date: Mon, 18 Nov 2013 16:38:41 +0000 > > > > > > Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 > > > > > > and CentOS 6 > > > > > > > > > > > > > > > > > > Dear FS experts, > > > > > > I have a question about compatibility for running recon-all > > > > > > (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac > > > > > > SnowLeopard OS X 10.6 (32b Intel). > > > > > > > > > > > > I already run recon all- for several of my subjects with a Mac > > > > > > Book Pro with Snow Leopard (using Release_I386 i386). As I have > > > > > > access to an additional machine (a linux CentOS 6 (64b)) I was > > > > > > wondering if I could process additional subjects in parallel > > > > > > with this other machine that are also intended to be included in > > > > > > the longitudinal stream. > > > > > > Also, I am not sure about whether I should be installing in the > > > > > > CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) > > > > > > because of compatibility issues. > > > > > > Thank you very much for your attention, > > > > > > Pablo > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer > > > > > > mailing list Freesurfer@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. > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@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. > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing > > > > > > list Freesurfer@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. > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.harvard.ed > > u> > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati > > on > > > 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. > > > >
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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.
