<div dir="ltr"><div><div><div><div>Hi Dan<br><br></div>If you use the -template option in tracks2prob with the FA image as the template, then yes, the transformation (at least the orientation component) will be identical to the FA image. The offset component of the transform will differ slightly if the voxel size is different in the TDI.<br>
<br></div>This question does however raise an important difference between MRtrix and other packages. The streamlines are generated and stored in 'real' / 'scanner' space, rather than with respect to any particular image space. To read an image value at a particular streamline position, the location is mapped according to the transform of that particular image. Therefore, it is not actually necessary for the ROI to be 'in the same space' (i.e. on the same voxel grid) as the image used to generate the streamlines; as long as the images are correctly aligned / registered, the streamline position in scanner space can be transformed to the appropriate location in the image volume.<br>
<br></div>Theoretically, you could have a ROI based on the FA image, a ROI based on the high-resolution TDI, and a ROI based on a (co-registered) anatomical image, and they could all be used in the same call to filter_tracks.<br>
<br>So if the purpose of the TDI is to identify a particular pathway and draw a ROI, it doesn't actually matter whether or not the -template option is provided to tracks2prob; the TDI will always be inherently aligned with the streamlines data, regardless of the alignment of the voxel grid. Though as an aside, you'll find the TDI file size will be much smaller if the -template option is <i>not</i> used, as it then uses the streamlines data to determine the required spatial extent of the image, so you don't get as much 'dead space' around the brain.<br>
<br></div>Happy holidays all<br>Rob<br></div><div class="gmail_extra"><br clear="all"><div><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith</b><br>Post-Doctoral Researcher, Imaging Division</span><br><br>The Florey Institute of Neuroscience and Mental Health<br>
Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div>
<br><br><div class="gmail_quote">On Sun, Dec 22, 2013 at 4:55 AM, Daniel Lumsden <span dir="ltr"><<a href="mailto:doclumsden@hotmail.com" target="_blank">doclumsden@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr">Dear All<br><br>I'm interested in using the improved resolution from track density images to help improve my ROI generation to select tracks from a whole brain tractography .tck file.<br><br>I can define, e.g., the PLIC much more sharply from the track density image generated from whole-brain tractography much more easily then from the standard colour coded FA maps. The orientation of the track density image depends upon the -template image supplied for tracks2prob step when generated. If I use the FA maps as the template, does this automatically put the ROI drawn from the resultant track density maps in diffusion space? If so I presume I can use these ROI to directly filter the streamlines I'm interested from the whole brain tractography .tck file without applying any transformation? <br>
<br>Many thanks in advance<br><br>Dan<br> </div></div>
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