Dear Juha,
The output image should be a 4D image with 9 volumes, each
containing the relevant information. This will all be contained
in one nii.gz file. Can you check that this is the case? Either
check with fslview or with fslsize (or fslhd). You need to look
at the dim4 value from output in the latter.
OK, so I guess that the memory requirements are indeed
the problem. It is possible that some of the third party
libraries might have an inbuilt 32bit limit. Can you tell me which
version you downloaded (e.g. was it a binary version and
what was the name of the downloaded file or option you
selected). With the memory that you have available it should
certainly be possible to get it to work, especially if it has managed
to get to the kernel multiplication stage.
All the best,
Mark
On 15 Apr 2010, at 14:41, Juha Pajula wrote:
> Hi,
>
> I tried now with 128x128x128 image and now the program runs in few
> minutes through without eny errors. It takes now even more memory
> from sge as earlier, so probably the memory was running out.
>
> Even this problen looks to be solved, it won't still do what I want.
> There is only one .nii.gz file in the output even if I have the --
> xyz flag in use.
>
> I need those outputs from --xyz to merge the B0 inhomogeneities for
> POSSUM.
>
> Any ideas where the problem is now?
>
> Mark Jenkinson wrote:
>> 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
>>>>>>>
>>>>>
>>>
>
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