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 > >
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