Dear Matt Glasser,
I typed "uname -m" in the terminal and it says "i686"
All the bests!
Sincerely,
Yonghui Li
Email: [log in to unmask] or [log in to unmask]
2009-11-05
======= 2009-11-05 10:40:01 :=======
>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
|