[Mrtrix-discussion] Export track files

Fri Jun 3 03:13:31 PDT 2011

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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