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FSL  March 2009

FSL March 2009

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Subject:

Re: memory in FSL 4.1*

From:

Lisa Lu <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 5 Mar 2009 18:52:48 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (143 lines)

Hi Steve,

I also get this message (Image Exception : #99 :: Out of memory
terminate called after throwing an instance of 'RBD_COMMON::BaseException')
when I run FAST (/usr/local/fsl/bin/fast -t 1 -n 3 )

We're also running on a 32-bit machine. I would appreciate learning about
fixes you guys come up with for 32-bit machine users.

Thanks,
Lisa Lu
University of Illinois at Chicago

On Thu, 5 Feb 2009 09:57:20 +0000, Steve Smith <[log in to unmask]>
wrote:

>Urgh - 32-bit! That probably explains the problem, but we can still
>have a quick look at your data.
>Cheers, Steve.
>
>
>On 5 Feb 2009, at 09:50, Mareike Menz wrote:
>
>> Dear Matthew,
>>
>> thanks again for your time.
>> I uploaded the directory and got the number 251845.
>> I also included the raw data in the directory.
>> By the way - we are still working on 32-bit architecture (and no
>> chance to change that soon),
>> nevertheless it worked before ;).
>>
>> Many regards,
>> Mareike
>>
>>
>>
>> Matthew Webster wrote:
>>> Hi,
>>> FSL4.1.2 does make additional fslstats calls, but I'm surprised
>>> it still crashes on the 4GB machine. Can you tar up the feat
>>> directory and upload it to:
>>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>> and let us know the 6-digit reference number?
>>> Many Regards
>>> Matthew
>>>> Dear FSL Team,
>>>>
>>>> We recently updated FSL from 4.0 to 4.12.
>>>> Ever since feat crashes during preprocessing with
>>>> Image Exception : #99 :: Out of memory
>>>> terminate called after throwing an instance of
>>>> 'RBD_COMMON::BaseException'
>>>> after /common/apps/fsl-412/bin/fslstats prefiltered_func_data_st -
>>>> k mask -p 50.
>>>>
>>>> This happens with exactly the same data I evaluated before, with
>>>> the same parameters - I only reopened the *fsf - files and resaved
>>>> them under Feat from FSL 4.12 (and changed location of MNI_152
>>>> etc.). I also use identical hardware (identical machine, maybe a
>>>> few updates) which worked well before (in December). The memory
>>>> load sums up to about 90% (1GB RAW) and then the process crashes.
>>>> Interestingly, this happened also with 4GB RAM, when I testes
>>>> different hardware.
>>>>
>>>> To us this looks like a strange memory conflict (maybe connected
>>>> to our configurations) and now we wonder if you changed anything
>>>> in memory handling between version 4.0 and version 4.1?
>>>>
>>>> Thanks for your help and greetings from Hamburg,
>>>> Mareike
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Mareike Menz
>>>> NeuroImage Nord Lübeck
>>>> University Medical Center Hamburg-Eppendorf, Bldg. S10
>>>> Martinistr. 52
>>>> 20246 Hamburg
>>>> Germany
>>>> +49 40 7410 53683
>>>> [log in to unmask]
>>>> -------------------------
>>>> () ascii ribbon campaign
>>>> /\ - against html mail
>>>>
>>>>
>>>> --
>>>> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und
>>>> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>>>>
>>>> Universitätsklinikum Hamburg-Eppendorf
>>>> Körperschaft des öffentlichen Rechts
>>>> Gerichtsstand: Hamburg
>>>>
>>>> Vorstandsmitglieder:
>>>> Prof. Dr. Jörg F. Debatin (Vorsitzender)
>>>> Dr. Alexander Kirstein
>>>> Ricarda Klein
>>>> Prof. Dr. Dr. Uwe Koch-Gromus
>>
>> --
>> Mareike Menz
>> NeuroImage Nord Lübeck
>> University Medical Center Hamburg-Eppendorf, Bldg. S10
>> Martinistr. 52
>> 20246 Hamburg
>> Germany
>> +49 40 7410 53683
>> [log in to unmask]
>> -------------------------
>> () ascii ribbon campaign
>> /\ - against html mail
>>
>>
>> --
>> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und
>> Genossenschaftsregister sowie das Unternehmensregister (EHUG):
>>
>> Universitätsklinikum Hamburg-Eppendorf
>> Körperschaft des öffentlichen Rechts
>> Gerichtsstand: Hamburg
>>
>> Vorstandsmitglieder:
>> Prof. Dr. Jörg F. Debatin (Vorsitzender)
>> Dr. Alexander Kirstein
>> Ricarda Klein
>> Prof. Dr. Dr. Uwe Koch-Gromus
>
>
>--------------------------------------------------------------------------
-
>Stephen M. Smith, Professor of Biomedical Engineering
>Associate Director, Oxford University FMRIB Centre
>
>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>+44 (0) 1865 222726 (fax 222717)
>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>--------------------------------------------------------------------------
-

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