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

[Robert Smith]

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
>
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