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<p class="MsoNormal"><span lang="EN-US">Hi Markus,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">MRtrix comes with a beautiful step by step manual on how to perform fiber tractography:
</span><a href="http://www.brain.org.au/software/mrtrix/tractography/index.html"><span lang="EN-US">http://www.brain.org.au/software/mrtrix/tractography/index.html</span></a><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The ‘streamtrack’ command also comes with an elaborate description:
</span><a href="http://www.brain.org.au/software/mrtrix/commands/streamtrack.html"><span lang="EN-US">http://www.brain.org.au/software/mrtrix/commands/streamtrack.html</span></a><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Looking into either of these documents will reveal that:
<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">‘streamtrack DT_STREAM’ does not take tensors as input, but DW images. If you supply the DW images as a nii file, it also requires that you specify a gradient table with the –grad argument.<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">‘streamtrack SD_STREAM’ does not take tensors as input (since it is not tensor based), but FOD spherical harmonic coefficients. A complete walkthrough on this is at
</span><a href="http://www.brain.org.au/software/mrtrix/tractography/index.html"><span lang="EN-US">http://www.brain.org.au/software/mrtrix/tractography/index.html</span></a><span lang="EN-US">.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Ben<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","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>Markus Gschwind<br>
<b>Sent:</b> zondag 13 november 2011 10:48<br>
<b>To:</b> mrtrix-discussion@public.nitrc.org<br>
<b>Subject:</b> [Mrtrix-discussion] streamtrack error<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal">Dear Mrtrix specialists,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I am completely new to Mrtrix and am trying to get it to work.<o:p></o:p></p>
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<p class="MsoNormal">When doing streamtrack commands however I seem to meet problems.<o:p></o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I tried both DT_STREAM and SD_STREAM, bot none of them worked.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Below please see the error messages.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I'd like to ask what seems wrong. Is it te tensor image itself? I created it using dwi2tensor form DICOM images.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The CC_mask.nii is a binary mask (1 layer), handdrawn on the corpus callosum.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Thanks in advance!<o:p></o:p></p>
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<p class="MsoNormal">Markus Gschwind<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">markus$ streamtrack -debug -info -seed CC_mask.nii DT_STREAM tensor.nii CC_tract<o:p></o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">streamtrack [INFO]: opening image "tensor.nii"...<o:p></o:p></p>
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<div>
<p class="MsoNormal">streamtrack [DEBUG]: preparing file "./tensor.nii"<o:p></o:p></p>
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<div>
<p class="MsoNormal">streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: sanitising transformation matrix...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: unmapping file "./tensor.nii"<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: setting up image "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: sanitising transformation matrix...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: setting up data increments for "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 704512 ]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: error parsing spherical ROI specification "CC_mask.nii" - assuming mask image<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: mapping image "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: data mapper for image "tensor.nii" mapped with segment size = 4227072 (optimised)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: launching 1 threads<o:p></o:p></p>
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<div>
<p class="MsoNormal">streamtrack [INFO]: found 0x0 diffusion-weighted encoding<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack: invalid gradient matrix dimensions<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: closing image "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: unmapping file "./tensor.nii"<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<div>
<p class="MsoNormal">Markus-Gschwinds-MacBook-Pro:Case_SSS markus$ streamtrack -debug -info -seed CC_mask.nii SD_STREAM tensor.nii CC_tract<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: opening image "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: preparing file "./tensor.nii"<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: sanitising transformation matrix...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: unmapping file "./tensor.nii"<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: setting up image "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: sanitising transformation matrix...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: setting up data increments for "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 704512 ]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: error parsing spherical ROI specification "CC_mask.nii" - assuming mask image<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: mapping image "tensor.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: file "./tensor.nii" mapped at 0x101000000, size 16908640 (read-only)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: data mapper for image "tensor.nii" mapped with segment size = 4227072 (optimised)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: launching 1 threads<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: opening image "CC_mask.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: preparing file "./CC_mask.nii"<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: file "./CC_mask.nii" mapped at 0x102021000, size 1409376 (read-only)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: sanitising transformation matrix...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: unmapping file "./CC_mask.nii"<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: setting up image "CC_mask.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: sanitising transformation matrix...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: setting up data increments for "CC_mask.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: data increments initialised with start = 0, stride = [ 1 128 16384 ]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: mapping image "CC_mask.nii"...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: file "./CC_mask.nii" mapped at 0x102021000, size 1409376 (read-only)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [DEBUG]: data mapper for image "CC_mask.nii" mapped with segment size = 704512<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">streamtrack [INFO]: failed to find SH peak!<o:p></o:p></p>
</div>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">-- <br>
<br>
<o:p></o:p></p>
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