Dear Luis,<br><br>It works and thank you so much!<br><br>There are more questions jumped into my mind:<br>Is it possible to convert the MRTRIX track files to ExploreDTI format (*.mat)?<br>Are there any data quality control and motion/distortion correction routines included in MRTRIX? <br>
And can MRTRIX deal with multiple b0 images? <br><br>Thank you again!<br><br>Best,<br><font color="#888888"><br>Yong</font><br><br><div class="gmail_quote">On Fri, Jun 3, 2011 at 10:31 AM, Luis Morís <span dir="ltr"><<a href="mailto:luis.moris.fernandez@gmail.com">luis.moris.fernandez@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Dear Yong,<br>
<br>
If you want to create a Track Density Image from a fiber file<br>
generated by the 'streamtrack' command you have to use 'tracks2prob'.<br>
In case you already have this TDI but in the mrtrix format, you can<br>
use either use 'mrconvert' to convert this file to Nifti format, or<br>
rerun 'tracks2prob' but in the ouputfile name use a file the extension<br>
'.nii'.<br>
<br>
Best,<br>
<br>
Luis.<br>
<div><div></div><div class="h5"><br>
On Fri, Jun 3, 2011 at 10:14 AM, Yong Li <<a href="mailto:yongli86@gmail.com">yongli86@gmail.com</a>> wrote:<br>
> Dear Ben & Donald,<br>
><br>
> Is it possible to export or convert MRTRIX fiber tracking files to Nifti<br>
> format? If so, how to execute? Thank you in advance!<br>
><br>
> Nice weekend!<br>
><br>
> Best regards,<br>
><br>
> Yong<br>
><br>
> On Fri, May 27, 2011 at 9:39 AM, Yong Li <<a href="mailto:yongli86@gmail.com">yongli86@gmail.com</a>> wrote:<br>
>><br>
>> Dear Thijs & Ben,<br>
>><br>
>> Thank you very much for your reply! It works as you suggested!<br>
>><br>
>> Have a nice weekend!<br>
>><br>
>> Yong<br>
>><br>
>>> Date: Wed, 25 May 2011 13:47:56 +0000<br>
>>> From: Jeurissen Ben <<a href="mailto:Ben.Jeurissen@ua.ac.be">Ben.Jeurissen@ua.ac.be</a>><br>
>>> Subject: RE: [Mrtrix-discussion] missing mrtrix.conf<br>
>>> (mrtrix-0.2.9-win32.exe on WinXP) and csdeconv error<br>
>>> To: "<a href="mailto:mrtrix-discussion@public.nitrc.org">mrtrix-discussion@public.nitrc.org</a>"<br>
>>> <<a href="mailto:mrtrix-discussion@public.nitrc.org">mrtrix-discussion@public.nitrc.org</a>><br>
>>> Message-ID:<br>
>>> <<a href="mailto:384E4D541D819449ABBBD507434317D10298E7@xmail30.ad.ua.ac.be">384E4D541D819449ABBBD507434317D10298E7@xmail30.ad.ua.ac.be</a>><br>
>>> Content-Type: text/plain; charset="us-ascii"<br>
>>><br>
>>> Indeed, the configuration file is a plain text file that has to be<br>
>>> created by the user (the same holds for the Linux version, so this is not a<br>
>>> Windows specific thing). For details on where to store the file, see<br>
>>> <a href="http://www.brain.org.au/software/mrtrix/appendix/config.html" target="_blank">http://www.brain.org.au/software/mrtrix/appendix/config.html</a>.<br>
>>><br>
>>> Cheers,<br>
>>> Ben<br>
>>><br>
>>> From: <a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a><br>
>>> [mailto:<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a>] On Behalf Of Thijs<br>
>>> Dhollander<br>
>>> Sent: dinsdag 24 mei 2011 19:41<br>
>>> To: <a href="mailto:mrtrix-discussion@public.nitrc.org">mrtrix-discussion@public.nitrc.org</a><br>
>>> Subject: RE: [Mrtrix-discussion] missing mrtrix.conf<br>
>>> (mrtrix-0.2.9-win32.exe on WinXP) and csdeconv error<br>
>>><br>
>>> Hi Yong Li,<br>
>>><br>
>>> I'm also running MRtrix since some time on WinXP. If I remember it<br>
>>> right, I think I created mrtrix.conf myself directly at C:\mrtrix.conf (i.e.<br>
>>> to be used system-wide).<br>
>>><br>
>>> About the "failed to converge" problem: you're probably using<br>
>>> super-resolved CSD inherently (because the SH order you picked has more<br>
>>> parameters than your acquired data). This problem should normally be less<br>
>>> severe or completely go away if you use a lower order (i.e. lower value for<br>
>>> lmax). If you only get a few of these errors, it's probably not even a<br>
>>> problem. ;-)<br>
>>> More info at: <a href="http://www.brain.org.au/software/mrtrix/faq.html#converge" target="_blank">http://www.brain.org.au/software/mrtrix/faq.html#converge</a><br>
>>><br>
>>> Kind regards,<br>
>>><br>
>>> Thijs Dhollander<br>
>>> PhD Student<br>
>>><br>
>>> <a href="mailto:thijs.dhollander@uz.kuleuven.ac.be">thijs.dhollander@uz.kuleuven.ac.be</a><br>
>>> tel. <a href="tel:%2B32%2016%2034%2090%2037" value="+3216349037">+32 16 34 90 37</a><br>
>>> gsm. <a href="tel:%2B32%20475%2036%2044%2027" value="+32475364427">+32 475 36 44 27</a><br>
>>><br>
>>> Medical Image Computing (K.U.Leuven, ESAT/PSI, MIC)<br>
>>> Medical Imaging Research Center | UZ Gasthuisberg | Herestraat 49 - bus<br>
>>> 7003 | B-3000 Leuven | <a href="http://www.medicalimagingcenter.be" target="_blank">http://www.medicalimagingcenter.be</a><br>
>>><br>
>>> From: <a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a><br>
>>> [mailto:<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a>] On Behalf Of Yong Li<br>
>>> Sent: dinsdag 24 mei 2011 17:51<br>
>>> To: <a href="mailto:mrtrix-discussion@public.nitrc.org">mrtrix-discussion@public.nitrc.org</a><br>
>>> Subject: [Mrtrix-discussion] missing mrtrix.conf (mrtrix-0.2.9-win32.exe<br>
>>> on WinXP) and csdeconv error<br>
>>><br>
>>> Dear Ben & Donald,<br>
>>><br>
>>> Thank you very much to develop such a nice software!<br>
>>><br>
>>> I just installed the mrtrix-0.2.9-win32.exe on WinXP. Is it true that<br>
>>> 'Windows installation' is stll 'Not yet supported'<br>
>>> (./MRtrix/doc/install/windows.html)? I do not find the mrtrix.conf<br>
>>> (./MRtrix/doc/appendix/config.html) file anywhere in my hard drive. Any idea<br>
>>> why and where please? My first try of analyzing my data was ok until the<br>
>>> csdeconv error-'csdeconv: failed to converge'. How could I correct this<br>
>>> error please? Is there a possibility to apply motion and distortion<br>
>>> correction in the preprocessiong? Thank you again!<br>
>>><br>
>>> Sincerely yours,<br>
>>><br>
>>> Yong Li, PhD<br>
>>> ----------------------------------------------<br>
>>> Dr. Yong Li, M.Sci.<br>
>>> Neurologische Klinik, Klinikum rechts der Isar<br>
>>> Technische Universitaet Muenchen<br>
>>> Ismaninger Str. 22, 81675 Muenchen<br>
>>> Email: <a href="mailto:Yong.Li@lrz.tu-muenchen.de">Yong.Li@lrz.tu-muenchen.de</a><mailto:<a href="mailto:Yong.Li@lrz.tu-muenchen.de">Yong.Li@lrz.tu-muenchen.de</a>>,<br>
>>> <a href="mailto:YongLi86@gmail.com">YongLi86@gmail.com</a><mailto:<a href="mailto:YongLi86@gmail.com">YongLi86@gmail.com</a>><br>
>><br>
><br>
><br>
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><br>
</blockquote></div><br>