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<http://publish.uwo.ca/%7Ejdrozd2/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
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