Hi,
That's unusual, as this machine seems to have plenty of
memory and it seems to have passed through the
difficult stages of creating the FFTs. Can you try it without
the --xyz option and see if that works?
All the best,
Mark
On 13 Apr 2010, at 19:06, Juha Pajula wrote:
> Hi!
>
> Last machine I used was our deparment computing cluster. The used
> node had 32 gb of RAM and 10gb of swap. The cluster is running with
> Redhat Enterprise Linux operating system and the used FSL is version
> 4.1.4.
>
> The image has 256x256x256 pixels with 1 mm cubic size.
>
> The outputs from the program are following:
> Normal output from the grid engine:
> ---
> Calculating Bz field
> Calculating kernel
> zero pad
> Forward FFT
> Forward FFT
> Kernel multiplication
> ---
>
> Error output from the grid engine:
> ---
> .
> .
> .
> .
> .
> .
> .
> .
> Image Exception : #99 :: Out of memory
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> #SPOOL PATH#/spool/outolintu16/job_scripts/38441: line 1: 8013
> Aborted b0calc -i #PATH#/JH645/
> JH_anat_kaannetty_atmask -o #PATH#/b0/JH_b0/JH_b0x --b0x=1 --b0y=0 --
> b0=0 --xyz --verbose
> ---
>
> I removed the paths from the error report, so don't care about
> #SPOOL PATH# and #PATH#.
>
>
>
> Mark Jenkinson kirjoitti:
>> Hi,
>>
>> Sounds like you are running out of memory for this.
>> What are the dimensions of your input image?
>> That is, how many voxels in each direction?
>>
>> And do you get any output from the command at all?
>>
>> It would also be useful to know how much RAM and swap
>> your machine has, and what type of machine and OS it is.
>>
>> All the best,
>> Mark
>>
>>
>> On 13 Apr 2010, at 15:43, Juha Pajula wrote:
>>
>>> Hi!
>>>
>>> I am trying to create my own B0 inhomogeneities file for POSSUM
>>> with b0calc and fslmerge. I have followed the instructions from
>>> POSSUM homepage but I can't get the results out while b0calc gives
>>> me an error:
>>>
>>> Image Exception : #99 :: Out of memory
>>>
>>> The used command is like the example at POSSUM homepage:
>>>
>>> b0calc -i JH_anat_atmask -o outputut/b0/JH_b0x --b0x=1 --b0y=0 --
>>> b0=0 --xyz --verbose
>>>
>>> I have tried to run this with separeted desktop computer as well
>>> as our department computing cluster via N1 Grid Engine. Both give
>>> the same result.
>>>
>>> The file JH_anat_atmask is in Analyze 7.5 format (with .hdr
>>> and .img files)
>>>
>>>
>>> Can you help me to solve the problem?
>>>
>>>
>>> --
>>>
>>> Juha Pajula,
>>> Research Assistant,
>>> Methods and Models for Biological Signals and Images group of Signal
>>> Processing department in Tampere University of Technology
>>>
>>> email: [log in to unmask]
>>> mobile: +358405426242
>>>
>
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