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

[Thijs Dhollander]

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<mailto: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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