I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut flag
I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that took only 10% more time than one recon-all alone. 2011/7/6 John Jan Drozd <john.dr...@gmail.com> > Hi Bruce, > > Thanks for pointing this out to me about the RAM. > > I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects > simultaneously if each subject requires 2 to 3 Gb of RAM. > > Thanks, > John > > Sent from my iPhone > > On 2011-07-05, at 6:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > > > how much ram do you have? You'll need at least 2G/subject if not 3 > > On Tue, 5 Jul 2011, John Drozd wrote: > > > >> Hi Bruce, > >> Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. > >> Take care, > >> John > >> 2011/7/5 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > >> Sorry, that won't help a single subject much, although there are > >> options to run the hemis in parallel. You can run multiple > >> subjects at the same time, which is what we usually do. Or you > >> can use cuss > >> On Jul 5, 2011, at 5:11 PM, John Drozd <john.dr...@gmail.com> wrote: > >> > >> Hi Bruce, > >> > >> Okay, thank you. I understand and can see that to do an > >> accurate job, the pipeline must be complicated. > >> I have eight processors on my linux desktop computer. > >> Maybe some parts of recon-all are multi-threaded which > >> could speed things up for me :-) > >> > >> Thank you, > >> John > >> > >> 2011/7/5 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > >> sorry, but the majority of the time is > >> required. We're working to speed things up, > >> but it is complicated software with multiple > >> nonlinear warps, segmentation procedures, > >> etc.... > >> Bruce > >> On Tue, 5 Jul 2011, John Drozd wrote: > >> > >> Hi Bruce and Pedro, > >> > >> Thank you both for sending me your > >> suggestions. > >> Just to let you know, because my .dcm (dicom) > >> files had a space and two dots > >> in the filenames: > >> (e.g. "2008_12_08.ek -0035-0001-00001.dcm" ) > >> (and using quotes around the file name or "\ " > >> within the filename without > >> the quotes did not work with recon-all), > >> recon-all truncated the filename > >> before the space as "2008_12_08.ek" feeding it > >> to an mri_convert command and > >> gave an error message. > >> > >> So I worked around this problem as follows: I > >> converted the .dcm series to a > >> nifti .nii volume using 3D Slicer, and then > >> used mri_convert to convert the > >> .nii format to .mgz format. Then I ran > >> recon-all on the .mgz formatted file > >> and it is now running successfully. > >> > >> I see on the online tutorials and slides, that > >> this process takes about 20 > >> hours. Is there a way to only run partial > >> steps pertaining only to the > >> cortical thickness? > >> > >> Pedro also suggested that I go through the > >> FreeSurferBeginnersGuide wiki > >> which I am doing now. > >> > >> Also, reading some mailing lists emails, I > >> noticed that matlab can be used > >> to analyze the cortical thickness statistiics, > >> and also freesurfer comes > >> with matlab scripts. I will try these tools > >> out as well. > >> > >> Thank you for your time, > >> John > >> > >> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl > >> <fis...@nmr.mgh.harvard.edu> > >> wrote: > >> recon-all \ > >> -i <one slice in the anatomical > >> dicom series> \ > >> -s <subject id that you make up> \ > >> -sd <directory to put the subject > >> folder in> \ > >> -all > >> > >> cheers > >> Bruce > >> > >> On Tue, 5 Jul 2011, John Drozd wrote: > >> > >> Hi, > >> > >> I am running freesurfer on 64 bit Fedora > >> 10 linux. > >> I am using version: > >> > >> freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. > >> Can anyone point me to a reference web > >> page listing what > >> steps I need to > >> type to process > >> a series of MRI dicom slices and use > >> FreeSurfer to measure > >> cortical > >> thickness for this dicom series? > >> > >> Thank you, > >> John > >> > >> -- > >> John Drozd > >> Post-Doctoral Fellow, Robarts Research > >> Institute > >> The University of Western Ontario > >> London, ON, Canada > >> http://publish.uwo.ca/~jdrozd2/index.htm > >> > >> > >> _______________________________________________ > >> 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. > >> > >> -- > >> John Drozd > >> Post-Doctoral Fellow, Robarts Research > >> Institute > >> The University of Western Ontario > >> London, ON, Canada > >> http://publish.uwo.ca/~jdrozd2/index.htm > >> > >> -- > >> John Drozd > >> Post-Doctoral Fellow, Robarts Research Institute > >> The University of Western Ontario > >> London, ON, Canada > >> http://publish.uwo.ca/~jdrozd2/index.htm > >> > >> -- > >> John Drozd > >> Post-Doctoral Fellow, Robarts Research Institute > >> The University of Western Ontario > >> London, ON, Canada > >> http://publish.uwo.ca/~jdrozd2/index.htm > >> > >> >
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