[Mrtrix-discussion] Export track files

[Luis Morís]

Dear Yong,

    If you want to create a Track Density Image from a fiber file
generated by the 'streamtrack' command you have to use 'tracks2prob'.
In case you already have this TDI but in the mrtrix format, you can
use either use 'mrconvert' to convert this file to Nifti format, or
rerun 'tracks2prob' but in the ouputfile name use a file the extension
'.nii'.

Best,

Luis.

On Fri, Jun 3, 2011 at 10:14 AM, Yong Li <yongli86 at gmail.com> wrote:
> Dear Ben & Donald,
>
> Is it possible to export or convert MRTRIX fiber tracking files to Nifti
> format? If so, how to execute? Thank you in advance!
>
> Nice weekend!
>
> Best regards,
>
> Yong
>
> On Fri, May 27, 2011 at 9:39 AM, Yong Li <yongli86 at gmail.com> wrote:
>>
>> Dear Thijs & Ben,
>>
>> Thank you very much for your reply! It works as you suggested!
>>
>> Have a nice weekend!
>>
>> Yong
>>
>>> Date: Wed, 25 May 2011 13:47:56 +0000
>>> From: Jeurissen Ben <Ben.Jeurissen at ua.ac.be>
>>> Subject: RE: [Mrtrix-discussion] missing mrtrix.conf
>>>        (mrtrix-0.2.9-win32.exe on      WinXP) and csdeconv error
>>> To: "mrtrix-discussion at public.nitrc.org"
>>>        <mrtrix-discussion at public.nitrc.org>
>>> Message-ID:
>>>        <384E4D541D819449ABBBD507434317D10298E7 at xmail30.ad.ua.ac.be>
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> Indeed, the configuration file is a plain text file that has to be
>>> created by the user (the same holds for the Linux version, so this is not a
>>> Windows specific thing).  For details on where to store the file, see
>>> http://www.brain.org.au/software/mrtrix/appendix/config.html.
>>>
>>> Cheers,
>>> Ben
>>>
>>> From: mrtrix-discussion-bounces at public.nitrc.org
>>> [mailto:mrtrix-discussion-bounces at public.nitrc.org] On Behalf Of Thijs
>>> Dhollander
>>> Sent: dinsdag 24 mei 2011 19:41
>>> To: mrtrix-discussion at public.nitrc.org
>>> Subject: RE: [Mrtrix-discussion] missing mrtrix.conf
>>> (mrtrix-0.2.9-win32.exe on WinXP) and csdeconv error
>>>
>>> Hi Yong Li,
>>>
>>> I'm also running MRtrix since some time on WinXP.  If I remember it
>>> right, I think I created mrtrix.conf myself directly at C:\mrtrix.conf (i.e.
>>> to be used system-wide).
>>>
>>> About the "failed to converge" problem: you're probably using
>>> super-resolved CSD inherently (because the SH order you picked has more
>>> parameters than your acquired data).  This problem should normally be less
>>> severe or completely go away if you use a lower order (i.e. lower value for
>>> lmax).  If you only get a few of these errors, it's probably not even a
>>> problem. ;-)
>>> More info at: http://www.brain.org.au/software/mrtrix/faq.html#converge
>>>
>>> Kind regards,
>>>
>>> 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 Yong Li
>>> Sent: dinsdag 24 mei 2011 17:51
>>> To: mrtrix-discussion at public.nitrc.org
>>> Subject: [Mrtrix-discussion] missing mrtrix.conf (mrtrix-0.2.9-win32.exe
>>> on WinXP) and csdeconv error
>>>
>>> Dear Ben & Donald,
>>>
>>> Thank you very much to develop such a nice software!
>>>
>>> I just installed the mrtrix-0.2.9-win32.exe on WinXP. Is it true that
>>> 'Windows installation' is stll 'Not yet supported'
>>> (./MRtrix/doc/install/windows.html)? I do not find the mrtrix.conf
>>> (./MRtrix/doc/appendix/config.html) file anywhere in my hard drive. Any idea
>>> why and where please? My first try of analyzing my data was ok until the
>>> csdeconv error-'csdeconv: failed to converge'. How could I correct this
>>> error please? Is there a possibility to apply motion and distortion
>>> correction in the preprocessiong? Thank you again!
>>>
>>> Sincerely yours,
>>>
>>> Yong Li, PhD
>>> ----------------------------------------------
>>> Dr. Yong Li, M.Sci.
>>> Neurologische Klinik, Klinikum rechts der Isar
>>> Technische Universitaet Muenchen
>>> Ismaninger Str. 22, 81675 Muenchen
>>> Email: Yong.Li at lrz.tu-muenchen.de<mailto:Yong.Li at lrz.tu-muenchen.de>,
>>> YongLi86 at gmail.com<mailto:YongLi86 at gmail.com>
>>
>
>
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