Hi Markus,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>1) >> track_info</div><div><br></div><div>is it possible read the count value into a variable? I tried with awk, like I do with some fsl functions:</div>
<div><br></div><div><div>track_info_output=`track_info L_SubstInn_CapsExt_tract.tck` </div></div><div><div>cout=`echo $count | awk '{print $1}'`</div></div><div><br></div><div>I take $1 because it is in the first line of the output.</div>
<div><br></div><div>However, I am puzzled to find the whole directory content in the $count.</div></blockquote><div><br></div><div>This works for me:</div><div><div>count=`track_info mytrack.tck | grep '\<count:' | awk '{ print $2 }'`</div>
</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><br></div><div>2) >> normalise_tracks</div><div><br></div><div>What type of warp image is needed here? I cannot find any specifications (the ideal would be to feed in the warps created by the fsl TBSS pipeline. Is there any hope?)</div>
</blockquote><div><br></div><div>Indeed, not a lot of information on this anywhere... It's the simplest thing I could think of: it's a 4D file (3 volumes), with each voxel reporting the coordinates of the position it maps to in the other space. </div>
<div><br></div><div>The idea behind that choice, besides simplicity, is to allow extraction of the warp field regardless of the normalisation package used - they all store the transformation information in different ways, so it's impossible to support them all directly. Essentially, it works by generating a 'no warp' image, simply by taking a given image and assigning to each voxel its own location in real/scanner coordinates - this is what gen_unit_warp does. Since this is a just like any other image, you can then use whichever package you used to estimate the warp (SPM, ANTS, FNIRT, etc) to apply the warp to the 'no-warp' image. The resulting warped image contains the required warp information, in the format expected by normalise_tracks: each voxel reports its original position.</div>
<div><br></div><div>For more information, there is an entry about it in the FAQ: <a href="http://www.brain.org.au/software/mrtrix/faq.html#normalise_tracks">http://www.brain.org.au/software/mrtrix/faq.html#normalise_tracks</a></div>
<div> </div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br></div><div>Thanks again and best wishes!</div><span class="HOEnZb"><font color="#888888"><div>Markus</div><div><br></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9035 7033<br>