Hi!
If the output is as you said they you have wrong instructions at POSSUM
homepage: http://www.fmrib.ox.ac.uk/fsl/possum/input.html#b0field
Also the results looks to be wrong. There is only three volumes in the file:
bash-3.2$ fslsize IJ_b0x.nii.gz
dim1 128
dim2 128
dim3 128
dim4 3
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 2.0000000000
pixdim4 1.0000000000
The used FSL war pre-build fsl-4.1.4-centos5_32.tar
Mark Jenkinson wrote:
> 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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