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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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