[Mrtrix-discussion] Export track files

Fri Jun 3 07:26:33 PDT 2011

Hello.

I do not have anything for ExploreDTI format, but this may be of help
for you or someone else. It converts the tracks to vtk format.

Cheers
.
Another Luis.

On Fri, Jun 3, 2011 at 6:13 AM, Yong Li <yongli86 at gmail.com> wrote:
> Dear Luis,
>
> It works and thank you so much!
>
> There are more questions jumped into my mind:
> Is it possible to convert the MRTRIX track files to ExploreDTI format
> (*.mat)?
> Are there any data quality control and motion/distortion correction routines
> included in MRTRIX?
> And can MRTRIX deal with multiple b0 images?
>
> Thank you again!
>
> Best,
>
> Yong
>
> On Fri, Jun 3, 2011 at 10:31 AM, Luis Morís <luis.moris.fernandez at gmail.com>
> wrote:
>>
>> 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>
>> >>
>> >
>> >
>> > _______________________________________________
>> > Mrtrix-discussion mailing list
>> > Mrtrix-discussion at www.nitrc.org
>> > http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>> >
>> >
>
>
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