[Mrtrix-discussion] "shbasis -convert" produces corrupted NIfTI

[Robert Smith]

Hi everybody,

Just a quick update to say that, once you pull the latest code updates and
recompile, shbasis should now work as expected with all compressed image
formats.

Cheers
Rob


--

*Robert Smith, Ph.D*
Research Officer, Imaging Division

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au

On Tue, Dec 16, 2014 at 12:44 AM, Robert Smith <robert.smith at florey.edu.au>
wrote:
>
> Hi Ulrike,
>
> The problem looks to be specific to the use of compressed image formats
> with the shbasis command (though I suspect any command that modifies an
> image in-place will suffer a similar fate).
> I'll dig into the problem when I get the chance, but for now the simplest
> fix is to convert to uncompressed NIfTI, run shbasis, then convert back to
> compressed format.
>
> Thanks for the report
> Rob
>
>
> --
>
> *Robert Smith, Ph.D*
> Research Officer, Imaging Division
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7128
> Fax: +61 3 9035 7301
> www.florey.edu.au
>
> On Mon, Dec 15, 2014 at 11:31 PM, Ulrike Kuhl <kuhl at cbs.mpg.de> wrote:
>>
>> Dear MRtrix Team,
>>
>> First of all thank you for your great tools - they have been of great
>> help to me during my tractography analysis so far. However, I've
>> encountered a problem when trying to convert the SH basis of my CSD data
>> computed with MRTrix 0.2 to the MRTrix3 version.
>> As I eventually want to use SIFT implemented in MRTrix3, I followed the
>> instructions in the wiki in order to convert the SH basis. Everything
>> appears to work fine when running the 'shbasis -convert native' command (no
>> warnings let alone error messages).
>> However, I cannot use the resulting converted data as the NifTI format is
>> not recognized anymore.
>> Calling 'mrview' results in:
>>
>> mrview: image "./my_CSD.nii.gz" is not in NIfTI format (magic != "n+1\0")
>> mrview: error opening image "my_CSD.nii.gz"
>>
>> Likewise I cannot open the resulting image in a differen viewer like
>> fslview.
>>
>> This occurs when using the 'native' as well as the 'forced_oldtonew'
>> choice.
>> Did you come across this problem before and do you have a suggestion on
>> how to overcome this issue?
>>
>> Thank you very much in advance!
>>
>> Best
>> Ulrike
>>
>> --
>> Max Planck Institute for Human Cognitive and Brain Sciences
>> Department of Neuropsychology (A220)
>> Stephanstraße 1a
>> 04103 Leipzig
>>
>> Phone: +49 (0) 341 9940 2586
>> Mail: kuhl at cbs.mpg.de
>> Internet: http://www.cbs.mpg.de/staff/kuhl-12160
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>
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