[Mrtrix-discussion] Question about filter_tracks command

[Robert Smith]

Hi Dan

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.

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.

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.

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 *not* 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.

Happy holidays all
Rob


--

*Robert Smith*
Post-Doctoral Researcher, Imaging Division

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au


On Sun, Dec 22, 2013 at 4:55 AM, Daniel Lumsden <doclumsden at hotmail.com>wrote:

> Dear All
>
> 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.
>
> 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?
>
> Many thanks in advance
>
> Dan
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20131222/eab1b94f/attachment.html>