That's a matter of personal preference, FSL should run fine on both!
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of YonghuiLi
Sent: Wednesday, November 04, 2009 9:17 PM
To: [log in to unmask]
Subject: Re: [FSL] Asking for your help about "probtrackx"
Dear Matt,
Thank you very much for solving our problem! We currently have a Centos-5-64 at hand, will it be OK if we reinstall our system to Centos-5-64? Or is it better to use the Ubuntu 64bit version?
All the bests!
Sincerely,
Yonghui Li
Email: [log in to unmask] or [log in to unmask]
2009-11-05
======= 2009-11-05 11:00:01 :=======
>That is the 32bit version of Ubuntu. Using it, you will not be able to address more than 4GB of RAM in total and not more than 2GB of RAM per process. This is why you are running out of memory. I would download the latest Ubuntu 64bit version.
>
>Peace,
>
>Matt.
>
>-----Original Message-----
>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of YonghuiLi
>Sent: Wednesday, November 04, 2009 8:49 PM
>To: [log in to unmask]
>Subject: Re: [FSL] Asking for your help about "probtrackx"
>
>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
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