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Hi,

What happens if you try to run it on a smaller image?
Say, just crop out a 128x128x128 portion of your existing
image and see what happens.

I'm quite puzzled by what you've found so far.

All the best,
	Mark


On 14 Apr 2010, at 17:20, Juha Pajula wrote:

> Hi
>
> The results are exactly same without --xyz flag.
>
> The exit signal from sge is 137 and by some search in web this looks  
> to mean that the used program, in this case b0calc, calls abort by  
> itself.
>
> According to sge logs the memory or swap is nor running out.
>
>
>
> Mark Jenkinson wrote:
>> 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
>>>>>
>>>
>