[Mrtrix-discussion] converting color TDI -DEC to nii

[René Besseling]

This should work:

fslmerge -t dec-tdi.nii dec-tdi-*.nii

On Wed, Jun 1, 2011 at 11:20 AM, Thijs Dhollander
<thijs.dhollander at uzleuven.be> wrote:
> Here you can download a tool that I use to get my Matlab-stuff into NIfTI:
>
>
>
> http://www.rotman-baycrest.on.ca/~jimmy/NIfTI/
>
> (also: http://www.mathworks.com/matlabcentral/fileexchange/8797 )
>
>
>
> Using this, you could import the 3 NIfTI files you get from mrconvert into
> Matlab, combine them into a 4D matrix, and then export it again as an RGB
> NIfTI.
>
> It's a bit cumbersome though, and I guess there must certainly be some other
> tools around that allow you to do this in a more direct way.
>
>
>
> Kind regards,
>
> Thijs
>
>
>
>
>
> Thijs Dhollander
> PhD Student
>
> thijs.dhollander at uz.kuleuven.ac.be
> tel. +32 16 34 90 37
> gsm. +32 475 36 44 27
>
> Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)
> Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus
> 7003 | B-3000 Leuven | http://www.medicalimagingcenter.be
>
>
>
> From: mrtrix-discussion-bounces at public.nitrc.org
> [mailto:mrtrix-discussion-bounces at public.nitrc.org] On Behalf Of Donald
> Tournier
> Sent: woensdag 1 juni 2011 9:03
> To: Nyoman Kurniawan
> Cc: mrtrix-discussion at www.nitrc.org
> Subject: Re: [Mrtrix-discussion] converting color TDI -DEC to nii
>
>
>
> Hi Nyoman,
>
>
>
> I'm guessing you're talking about converting into the RGB format supported
> by NIfTI. Unfortunately there is no support for that in MRtrix. The best you
> could do currently would be to export each RGB channel separately, using a
> command such as this:
>
>
>
> $ mrconvert dec-tdi.mif dec-tdi-[].nii
>
>
>
> The empty square brackets will tell MRtrix to split up the last dimension of
> the image into separate files, so that should give
> you dec-tdi-0.nii, dec-tdi-1.nii and dec-tdi-2.nii, corresponding to red,
> green and blue respectively.
>
>
>
> I have no idea if that is useful to you, since I'm guessing you would still
> need to recombine these channels into a single RGB NIfTI image. Hopefully
> there is something in the NIfTI tools that can do that, but I've never
> looked into it myself...
>
>
>
> If you do manage to get it done, it would be great if you could report how
> you did it here, it might be helpful to other users too.
>
>
>
> Cheers,
>
>
>
> Donald.
>
>
>
>
>
>
>
> On 1 June 2011 16:43, Nyoman Kurniawan <nyoman.kurniawan at cai.uq.edu.au>
> wrote:
>
> Dear Donald & Fernando,
>
> Could you tell me how to use mrconvert to convert the colour TDI-DEC into
> the nii format?
>
> I could only convert it into a grey scale nii.
>
>
>
> Thank you.
>
>
>
> Regards,
>
> Nyoman
>
>
>
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>
> --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9035 7033
>
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