[Mrtrix-discussion] Question about filter_tracks command

Daniel Lumsden doclumsden at hotmail.com
Sun Jan 12 11:14:17 PST 2014


Thank you for a very helpful answer - apologies for slow acknowledgement and reply!

Given that mrtrix generates streamlines in "real space", does this mean that I could create a seed region from an anatomical image converted from the dicom to nifti using mrconvert, then supply that mask directly to streamtrack?

I've been creating mask images from reasonably high resolution T1 images, then using the linear transform generated by flirt in FSL (transform of structural scan to diffusion scan) to transform these mask images into the much lower resolution diffusion space.  

If I can supply the seed directly, could I then use my T1 image as the template for tracks2prob to visualise the track density on the scans without needing to apply any transformation?

I hope this isn't a hopelessly naive question!


Date: Sun, 22 Dec 2013 10:37:52 +1100
Subject: Re: [Mrtrix-discussion] Question about filter_tracks command
From: r.smith at brain.org.au
To: doclumsden at hotmail.com
CC: mrtrix-discussion at www.nitrc.org

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


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

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



Mrtrix-discussion mailing list

Mrtrix-discussion at www.nitrc.org


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20140112/51e39628/attachment.html>

More information about the Mrtrix-discussion mailing list