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.drozd@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 <fischl@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 <fischl@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
      



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--
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