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</o:shapelayout></xml><![endif]--></head><body lang=NL-BE link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Hi Mchandra,<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><p class=MsoNormal><span lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>While I just started to type an answer, I noticed myself how you probably got confused about the arguments and options for the tracks2prob command. <b><u>I'm going to assume you have the latest 0.2.9 version of MRtrix.</u></b> I just noticed the online version of the documentation is outdated, and some important things about tracks2prob have changed since that version. You should check out the documentation that came with your version in .../MRtrix/doc/commands/tracks2prob.html (where "..." is the folder you installed it to).<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 lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>Some (random) info and answers:<o:p></o:p></span></b></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'>(1) From the online version of the documentation, compared to the documentation that comes with 0.2.9: tracks2prob used to have 3 arguments (tracks, template, output), but now it only has 2 (tracks, output). "-template" became an option instead of an argument. BUT... it seems you still NEED to supply a template (as a "-template"), i.e. also in the case you want to do a higher resolution TDI-like operation. This explains your "No error" errors (I once got the same ones until I discovered this fact). When you do a higher resolution with the "-vox" option, you still need to specify the "-template" option. The latter one is now only used as a "field of view", while the "-vox" option is used for the resolution.<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'>(2) There used to be a "-count" option, to override the default calculation of fractions. In 0.2.9, this is the other way around (!): now there is a "-fraction" option, while the default behaviour is the absolute count. This explains your "unknown option "count"" error.<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 lang=EN-US style='font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D'>So fixed versions of both your commands would be:<o:p></o:p></span></b></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'>(1) tracks2prob -template sometemplate.mif -vox 1 -fraction whole_brain_tracks.tck fraction_tracks.mif<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'>(2) tracks2prob -template anat.img whole_brain_tracks.tck track_counts.mif<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'>For "sometemplate.mif" in the first one, I guess you might want to use "anat.img".<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'>One last warning for the higher resolution one: depending on how much memory your machine has, you might run out of it. To circumvent this in some way, you can create a new template (from your previous template) using a combination of "mrconvert" and "mrtransform" (with the "-replace" option), that has a smaller "field of view" (for instance: half the brain, some slices, etc...).<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'><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>mchandra pal<br><b>Sent:</b> dinsdag 24 mei 2011 22:02<br><b>To:</b> mrtrix-discussion@public.nitrc.org<br><b>Subject:</b> [Mrtrix-discussion] Higher resolution TDI<o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi,<o:p></o:p></p></div><div><p class=MsoNormal>I have two queries. <o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>In the discussion forum, it was previously suggested that super-resolution TDI images can be generated using "-vox" option in tracks2prob command.<o:p></o:p></p></div><div><p class=MsoNormal>I used the commeand tracks2prob whole_brain_tracks.tck -vox 1 fraction_tracks.mif to obtain TDI image with 1 mm X 1mm x 1mm spatial resolution.<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>It shows:<o:p></o:p></p></div><div><p class=MsoNormal>tracks2prob: creating new template image... - ok<br>tracks2prob: error opening tracks data file "whole_brain_tracks.tck": No error<br>tracks2prob: error opening tracks data file "whole_brain_tracks.tck": No error<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Also, when I tried to generate TDI image with the fibre count through each voxel using option 'count' (e.g. tracks2prob whole_brain_tracks.tck -count -template anat.img track_counts.mif), it shows<o:p></o:p></p></div><div><p class=MsoNormal>tracks2prob: unknown option "count".<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Please kindly suggest the correct ways to write these commands.<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>-mc pal<o:p></o:p></p></div></div></body></html>