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 BruceOn 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