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</o:shapelayout></xml><![endif]--></head><body lang=NL-BE link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Here you can download a tool that I use to get my Matlab-stuff into NIfTI:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'><a href="http://www.rotman-baycrest.on.ca/~jimmy/NIfTI/">http://www.rotman-baycrest.on.ca/~jimmy/NIfTI/</a><o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>(also: <a href="http://www.mathworks.com/matlabcentral/fileexchange/8797">http://www.mathworks.com/matlabcentral/fileexchange/8797</a> )<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>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.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>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.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Kind regards,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Thijs<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#00A1D6'>Thijs Dhollander</span></b><span style='font-family:"Arial","sans-serif";color:#1F497D'><br></span><span style='font-size:10.5pt;font-family:"Arial","sans-serif";color:#666666'>PhD Student</span><span style='font-family:"Arial","sans-serif";color:#1F497D'><br></span><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:#1F497D'><br></span><span style='font-size:9.0pt;font-family:"Arial","sans-serif";color:#666666'>thijs.dhollander@uz.kuleuven.ac.be<br>tel. +32 16 34 90 37<br>gsm. +32 475 36 44 27</span><b><span style='font-size:8.0pt;font-family:"Arial","sans-serif";color:#00A1D6'><br><br>Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)<br></span></b><span style='font-size:8.0pt;font-family:"Arial","sans-serif";color:#666666'>Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus 7003 | B-3000 Leuven | http://www.medicalimagingcenter.be</span><span style='font-size:11.0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> mrtrix-discussion-bounces@public.nitrc.org [mailto:mrtrix-discussion-bounces@public.nitrc.org] <b>On Behalf Of </b>Donald Tournier<br><b>Sent:</b> woensdag 1 juni 2011 9:03<br><b>To:</b> Nyoman Kurniawan<br><b>Cc:</b> mrtrix-discussion@www.nitrc.org<br><b>Subject:</b> Re: [Mrtrix-discussion] converting color TDI -DEC to nii<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Nyoman,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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:<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>$ mrconvert dec-tdi.mif dec-tdi-[].nii<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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... <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>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.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Cheers,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Donald.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On 1 June 2011 16:43, Nyoman Kurniawan <<a href="mailto:nyoman.kurniawan@cai.uq.edu.au">nyoman.kurniawan@cai.uq.edu.au</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'>Dear Donald & Fernando,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'>Could you tell me how to use mrconvert to convert the colour TDI-DEC into the nii format?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'>I could only convert it into a grey scale nii.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'>Thank you.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'>Regards,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'>Nyoman<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:8.5pt;font-family:"Calibri","sans-serif";color:black'><o:p> </o:p></span></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><br>_______________________________________________<br>Mrtrix-discussion mailing list<br><a href="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</a><br><a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><o:p></o:p></p></div><p class=MsoNormal><br><br clear=all><br>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9035 7033<o:p></o:p></p></div></div></body></html>