Type uname -m in the terminal and paste what it says. Ubuntu has a 64bit version (which I use), if you want to stay with Ubuntu.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of YonghuiLi
Sent: Wednesday, November 04, 2009 8:34 PM
To: [log in to unmask]
Subject: Re: [FSL] Asking for your help about "probtrackx"
Dear Matt Glasser,
My system Info is "Ubuntu Release 8.04(hardy), Kernel Linux 2.6.29.3-custom GNOME 2.22.2". Will it help if I reinstall a Centos-5-64 system?
Email: [log in to unmask] or [log in to unmask]
2009-11-05
======= 2009-11-05 09:52:21 :=======
>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
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