[Mrtrix-discussion] Open ROI with fslview or freeview

[Thijs Dhollander]

Hi Arnaud,

The reason this tends to happen when trying to use ROIs created with MRtrix
in another software package, is the fact that the latter does not support
the bitwise datatype that MRtrix creates its ROIs with.
The solution is easy: just convert your ROIs to another datatype using
mrconvert with the "-datatype" option (see
http://www.brain.org.au/software/mrtrix/commands/mrconvert.html ).  The
available datatypes and the accompanying specifiers that should be used
with the "-datatype" option, can be found at
http://www.brain.org.au/software/mrtrix/general/formats.html .
You could run, e.g.:

mrconvert -datatype Int8 myROIcreatedwithMRtrix.mif myROItobeusedwithFSL.nii

Hope that's somewhat clear and solves your problem!

Cheers,
Thijs

*Thijs Dhollander
thijs.dhollander at gmail.com
Tel. +32 475 36 44 27*
Medical Image Computing (MIC), ESAT-PSI, Department of Electrical
Engineering, KU Leuven


On Fri, Sep 20, 2013 at 9:33 PM, Arnaud Boré <arnaud.bore at gmail.com> wrote:

> Dear Mrtrix experts,
>
> I've got an error when I create and save a ROI and then try to load it in
> FSL fslview (4.0.1) .
>
> This is the error message:
> nifti_convert_nhdr2nim: bad datatype
>
> I've got the same kind of problem when I try to load it with freeview
> unsupported datatype 1 with scl_slope !=0
>
> I'm using mrview 0.2.12 (revision 393)
>
> I tried the patch here :
> http://www.nitrc.org/pipermail/mrtrix-discussion/2012-April/000398.htmlbut didn't fix anything or maybe I've done it wrong
>
> Thank you for your help
>
> Arnaud
>
> --
> Arnaud BORE
> Research assistant
> Cellulaire : (001) 514-647-8649
>
>
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>
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