[Mrtrix-discussion] Re: Converting Fraction Images to Nifti

Donald Tournier d.tournier at brain.org.au
Tue Jun 19 16:17:03 PDT 2012


Hi Jason,

OK, not a memory issue, and error message is not helpful. Any chance you
could send me a file that works and one that doesn't? I might be able to
figure it out if I have the data. Or at least rule out the possibility that
this might be caused by MRtrix...

Cheers,

Donald.


On 20 June 2012 03:41, Langley, Jason Allen <jason.langley at emory.edu> wrote:

>  Hi Donald,
>
>  The size of the files are only about 30 MB so memory is not an issue.
>
>  The error message that is displayed in the terminal is
> fslview: line 6: 8608 Segmentation fault ${FSLDIR}/bin/fslview_bin $@
>
>  The number 8608 changes for each instance of the fault and sometimes
> (core dumped) will appear in the error message as well.
>
>  Thanks,
> Jason
>
>  ------------------------------
> *From:* Donald Tournier [d.tournier at brain.org.au]
> *Sent:* Monday, June 18, 2012 8:07 PM
> *To:* Langley, Jason Allen
> *Cc:* mrtrix-discussion at www.nitrc.org
>
> *Subject:* Re: Converting Fraction Images to Nifti
>
>  Hi Jason,
>
>  OK, if the issue isn't datatype-related (i.e. if a command like
> "mrconvert output.mif -datatype int16 output.nii" doesn't produce an image
> you can load in fslview), then the issue might be related to memory. How
> large is the image you're having trouble with? There's a good chance it
> won't load if it's larger than 2GB, and fslview is compiled in 32-bit mode.
> Also, can you confirm that fslview crashes with no other information than
> 'segmentation fault'? On my system, an unexpected datatype causes fslview
> to crash with a failed assertion message:
>
>   *fslview: /usr/include/boost/smart_ptr/shared_ptr.hpp:418: T*
> boost::shared_ptr< <template-parameter-1-1> >::operator->() const [with T =
> OverlayList]: Assertion `px != 0' failed.*
>
>
>  which at least gives the *very* informed user some clue as to what might
> conceivable be the problem. A message such as 'std::bad_alloc' would
> already be a big clue...
>
>  Cheers,
>
>  Donald.
>
>
> On 19 June 2012 08:21, Langley, Jason Allen <jason.langley at emory.edu>wrote:
>
>>  Hi Donald,
>>
>> Oddly enough, the issue only occurs with the fraction images
>> (connectivity / TDI maps?). I am able to convert other .mif images (FA maps
>> for example) to .nii and read those images into FSL or other imaging
>> programs. The segmentation fault only occurs when I convert a fraction
>> image from .mif to .nii . I have tried all of the datatype options listed
>> in the source of mrconvert.cpp and none seem to work.
>>
>> I have noticed some issues between the other .mif images and the fraction
>> images. When looking at the images in a hex editor, the FA maps (and other
>> .mif images) seem to have nonzero values in each byte where as in the
>> fraction image, only the first byte in each group is nonzero. I have
>> attached an image that illustrates this with a FA map (in the terminal on
>> the left) and a fraction image (in the terminal on the right). However, I
>> am not sure if this is an issue.
>>
>> Best,
>> Jason
>>  ------------------------------
>> *From:* Donald Tournier [d.tournier at brain.org.au]
>> *Sent:* Sunday, June 17, 2012 8:25 PM
>> *To:* Langley, Jason Allen
>> *Subject:* Re: Converting Fraction Images to Nifti
>>
>>   Hi Jason,
>>
>>  This is not an uncommon issue. Basically, most packages don't support
>> the full set of datatypes allowed in the NIfTI specification, whereas
>> MRtrix does. If it produces an image using one of those datatypes, other
>> packages won't be able to handle it. In the case of FSL, rather than
>> detecting this case and reporting it, it typically just segfaults without
>> any useful information. In any case, you can easily get around this using
>> the -datatype option of mrconvert, with a datatype supported by FSL. In my
>> experience, the set of datatypes that will work are: uint8, int16, int32,
>> float32 & float64.
>>
>> On a different note: can I ask you to post these kinds of questions on
>> the MRtrix mailing list? You can find it at:
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion. This way other
>> users might also benefit...
>>
>> Hope this helps.
>> Cheers,
>>
>>  Donald.
>>
>>
>> On 16 June 2012 02:24, Langley, Jason Allen <jason.langley at emory.edu>wrote:
>>
>>>  Dear Donald,
>>>
>>> I'm having issues reading converted fraction images. My processing steps
>>> are as follows:
>>> (1) Preprocessing and then fibre tracking using streamtrack
>>> (2) Creation of the fraction image from the tracks using tracks2prob
>>> (3) Conversion of the fraction image from .mif to .nii using mrconvert
>>>
>>> After the conversion, I am unable to read the resultant .nii file in
>>> FSL, Afni, SPM, ... . For example, if I use fslview to read the converted
>>> fraction image, an error saying 'Segmentation fault' will appear in the
>>> terminal.
>>>
>>> So far, I've only had this issue with the fraction images and other
>>> images (FA maps, masks, etc) that I convert can be read in other viewers.
>>> Do you have any thoughts / solutions to this issue?
>>>
>>> Thanks,
>>> Jason
>>>
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>>
>>
>>
>>  --
>> Jacques-Donald Tournier (PhD)
>> Brain Research Institute, Melbourne, Australia
>> Tel: +61 (0)3 9035 7033
>>
>
>
>
>  --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033
>



-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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