I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut flag
I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that took only 10% more time than one recon-all alone.
2011/7/6 John Jan Drozd john.drozd@gmail.com
Hi Bruce,
Thanks for pointing this out to me about the RAM.
I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects simultaneously if each subject requires 2 to 3 Gb of RAM.
Thanks, John
Sent from my iPhone
On 2011-07-05, at 6:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
how much ram do you have? You'll need at least 2G/subject if not 3 On Tue, 5 Jul 2011, John Drozd wrote:
Hi Bruce, Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. Take care, John 2011/7/5 Bruce Fischl fischl@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.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
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
-- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm