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
>>
>>
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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
>>
>> --
>> John Drozd
>> Post-Doctoral Fellow, Robarts Research Institute
>> The University of Western Ontario
>> London, ON, Canada
>>
http://publish.uwo.ca/~jdrozd2/index.htm
>>
>>