Are you also running a 64bit OS?
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of YonghuiLi
Sent: Wednesday, November 04, 2009 7:44 PM
To: [log in to unmask]
Subject: Re: [FSL] Asking for your help about "probtrackx"
Dear Saad,
I have 16GB RAM in my computer, so I am confused here why there is still "out of memory". Your help will be highly appreciated.
Thanks
Yonghui
Email: [log in to unmask]
2009-11-05
======= 2009-11-04 22:23:19 ：=======
>In your case roughly 4GB of RAM.
>
>Internally, probtrackx will use six times 50 volumes, each volume
>being 256x256x31*sizeof(float).
>(+ more if you specify waypoints/targets etc.)
>
>Saad.
>ps: if you can avoid upsampling the original data, that would save you
>a lot of RAM.
>
>
>
>On 4 Nov 2009, at 13:26, Yonghui Li wrote:
>
>> Dear FSL,
>>
>> I am sure that I set the input directory for probtrackx correctly,
>> which should be the output directory of BEDPOSTX (im my case, it is
>> bedpostx.bedpostX). So, can I assume that the suggestion of Saad is
>> the solution for my problem? More RAM will do the job? How many RAM
>> is required to run probtrackx? The dimension of my 4D data is
>> 256*256*45*31, voxel size 1*1*3.
>>
>> Best
>> Yonghui
>>
>>
>> Hi Yonghui Li
>> This is a RAM problem. You need to run probtrackx on a computer with
>> more RAM.
>>
>> Cheers,
>> Saad.
>>
>>
>>
>>
>> > Hi Yonghui,
>>
>> >
>>
>> > The the folder bedpostx.bedpostX seems fine so far.
>>
>> >
>>
>> > However when running Probtrackx you need to select the
>> bedpostx.bedpostX -
>>
>> > folder, not the BEDPOSTX folder, as you want to use the OUTPUT from
>>
>> > bedpostx, not the input in order to execute Probtrackx.
>>
>> >
>>
>> > Does this help?
>>
>> >
>>
>> > Cheers,
>>
>> > Markus
>>
>> >
>>
>> >
>>
>> > 2009/11/4 YonghuiLi <[log in to unmask]>
>>
>> >
>>
>> > > Dear Markus
>>
>> > >
>>
>> > > a) I run the "probtrackx" through the GUI window. I first set
>> the BEDPOSTX
>>
>> > > directory, then I set the X Y Z coordinate to one single voxel I
>> am
>>
>> > > interested in, then I "GO".
>>
>> > >
>>
>> > > b) I set the name of input directory for "bedpostx" step is
>> "bedpostx", so
>>
>> > > after it is done, the output directory is "bedpostx.bedpostX".
>> When doing
>>
>> > > "ls bedpostx.bedpostX", it shows the following ifnormation:
>>
>> > > bvals mean_f2samples.nii.gz
>> merged_ph1samples.nii.gz
>>
>> > > bvecs mean_ph1samples.nii.gz
>> merged_ph2samples.nii.gz
>>
>> > > commands.txt mean_ph2samples.nii.gz
>> merged_th1samples.nii.gz
>>
>> > > dyads1.nii.gz mean_th1samples.nii.gz
>> merged_th2samples.nii.gz
>>
>> > > dyads2.nii.gz mean_th2samples.nii.gz monitor
>>
>> > > logs merged_f1samples.nii.gz
>> nodif_brain_mask.nii.gz
>>
>> > > mean_f1samples.nii.gz merged_f2samples.nii.gz xfms
>>
>> > >
>>
>> > > Thank you very much for your help!
>>
>> > > Best
>>
>> > > Yonghui
>>
>> > >
>>
>> > >
>>
>> > > ======== 2009-11-03 18:14:06 您在来信中写道： ========
>>
>> > >
>>
>> > >
>>
>> > > Hi!
>>
>> > >
>>
>> > > In order to help, we need to know more. Can you post
>>
>> > > a) the probtrackx command you run?
>>
>> > > b) what you get when doing "ls <your_bedpostx.bedpost>"
>>
>> > >
>>
>> > > It is most likely that there is a file missing or has the wrong
>> name or the
>>
>> > > wrong path...
>>
>> > >
>>
>> > > Hth,
>>
>> > > Markus
>>
>> > >
>>
>> > >
>>
>> > > 2009/11/3 YonghuiLi <[log in to unmask]>
>>
>> > >
>>
>> > >> Dear FSL,
>>
>> > >>
>>
>> > >> I run into some troubles while try to do the probtrackx on
>> single voxel.
>>
>> > >> The "eddycurrent" and "bedpostx" steps are completed. Then I
>> continued the
>>
>> > >> "probtrackx" by enter the coordinate of a single seed voxel.
>> Then "GO". But
>>
>> > >> it stopped very soon, showing an error message:
>>
>> > >> "Errors: Image Exception: #99 :: Out of memory
>>
>> > >> terminate called after throwing an instance of
>>
>> > >> 'RBD_COMMON::BaseException'
>>
>> > >> Then the whole procedure stopped.
>>
>> > >>
>>
>> > >> Your help to my situation here will be highly appreciated.
>>
>> > >>
>>
>> > >> All the bests!
>>
>> > >>
>>
>> > >> Sincerely,
>>
>> > >> Yonghui Li
>>
>> > >>
>>
>> > >> Email: [log in to unmask]
>>
>> > >> 2009-11-03
>>
>> > >>
>>
>> > >
>>
>> > >
>>
>> > >
>>
>> > > --
>>
>> > >
>>
>> > >
>>
>> > > Dr. med. Markus Gschwind, M.D.
>>
>> > > Laboratory for Neurology and Imaging of Cognition - Dept of
>> Neurosciences
>>
>> > > University Medical Center (CMU)
>>
>> > > 1, Michel-Servet
>>
>> > > CH-1211 GENEVA - Switzerland
>>
>> > >
>>
>> > > Tel 0041 (0) 22 379 5324
>>
>> > > Fax 0041 (0) 22 379 5402
>>
>> > > email: [log in to unmask]
>>
>> > > http://labnic.unige.ch
>>
>> > >
>>
>> > > = = = = = = = = = = = = = = = = = = = = = =
>>
>> > >
>>
>> > > 致
>>
>> > > 礼！
>>
>> > >
>>
>> > > *Yonghui Li,* PhD, PostDoc
>>
>> > >
>>
>> > > LIAMA Center for Computational Medicine (CMC)
>>
>> > > National Laboratory of Pattern Recognition (NLPR)
>>
>> > > Institute of Automation, Chinese Academy of Sciences (CASIA)
>>
>> > > 95 Zhong Guan Cun East Road, Hai Dian District, Beijing 100190,
>> P.R.China
>>
>> > > Tel: +86-10-62659278
>>
>> > > Fax: +86-10-62551993
>>
>> > >
>>
>> > > National Reserach Center for Intelligent Computing Systems (NCIC)
>>
>> > > Institute of Computing Technology, Chinese Academy of Sciences
>> (ICT)
>>
>> > > 6 Ke Xue Yuan South Road, Hai Dian District, Beijing 100190,
>> P.R.China
>>
>> > >
>>
>> > > Email: [log in to unmask] or [log in to unmask] <[log in to unmask]
>> >
>>
>> > > [log in to unmask]
>>
>> > > 2009-11-04
>>
>> > >
>>
>> > >
>>
>> >
>>
>> >
>>
>> >
>>
>> > --
>>
>> >
>>
>> >
>>
>> > Dr. med. Markus Gschwind, M.D.
>>
>> > Laboratory for Neurology and Imaging of Cognition - Dept of
>> Neurosciences
>>
>> > University Medical Center (CMU)
>>
>> > 1, Michel-Servet
>>
>> > CH-1211 GENEVA - Switzerland
>>
>> >
>>
>> > Tel 0041 (0) 22 379 5324
>>
>> > Fax 0041 (0) 22 379 5402
>>
>> > email: [log in to unmask]
>>
>> > http://labnic.unige.ch
>>
>> >
>>
>>
>>
>>
>
>--
>Saad Jbabdi
>University of Oxford, FMRIB Centre
>
>JR Hospital, Headington, OX3 9DU, UK
>+44 (0) 1865 222523 (fax 717)
>www.fmrib.ox.ac.uk/~saad
|
