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

[Donald Tournier]

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
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