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> > 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> >>> 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/%7Ejdrozd2/index.htm> >>> http://publish.uwo.ca/~**jdrozd2/index.htm >>> >>> >>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> <Freesurfer@nmr.mgh.harvard.edu>Freesurfer@nmr.mgh.harvard.edu >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> 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>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/%7Ejdrozd2/index.htm>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/%7Ejdrozd2/index.htm> > 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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