Can someone explain me how to use DTI interpolated tracking?

PeterK · Post by **PeterK** » Wed Aug 11, 2004 8:23 pm

Can someone please explain me how to use the FACT method?
My anisotropy maps look fairly good. I select a tracking section. I select a few "starting point" somewhere in corpus collosum - but the bundles generated are empty.

What am I doing wrong. Am I supposed to "paint" the track? Is FA threshold of 0.0 an acceptable one? Or what am I doing wrong?

Post by **riviere** » Mon Aug 16, 2004 11:19 am

Have you made sure you saved the starting point regions ? (you just have to select "save" in the "session" menu of the ROI box in Anatomist, or hit ctrl-S).
I don't use the tracking module every day (Yann is on holiday and will be back in about 3 weeks) but as far as I see when I try it, it seems to work.
Denis

PeterK · Post by **PeterK** » Wed Aug 18, 2004 1:37 am

riviere wrote:Have you made sure you saved the starting point regions ? (you just have to select "save" in the "session" menu of the ROI box in Anatomist, or hit ctrl-S).
I don't use the tracking module every day (Yann is on holiday and will be back in about 3 weeks) but as far as I see when I try it, it seems to work.
Denis

Can you elaborate on the meaning of ROIs.
Is it the beginning point? Should I paint the entire track? What guides the selection of ROI?

Zahir Momin · Post by **Zahir Momin** » Wed Aug 18, 2004 5:59 am

You should go through the pipeline or manually under diffusion menu's and create all the necessary FA, ADC, VR maps and such. When you want to do DTI interpolated tracking you will need to specify starting points. This is a seed from which tracks will be drawn. To pick this open FA map(any of the maps) under anatomist. Visualize the map on the screen. Open its toolbox. Go to last tab. Make a new Session. Make a new region. Now draw the region on the map(play around with drawing regions, this can be tricky). Choose a small region to include either internal capsule, corpus callosus, or any white matter region that is not too large. Right click on the chosen region and select it. Browser window will come up. In the browser, right click on RoiArg and save it to a file anywhere. In DTI tracking, you specify this file as starting points.
The tracking session folder can be any, as far as I can tell.

This is how i do it. Others may do it differently.

Post by **riviere** » Wed Aug 18, 2004 10:46 am

Zahir is right, but there is also a more easy way to initialize the drawing part for tracking: in BrainVisa, the "starting points" parameter is the filename to the ROI, there is a "pen" button which directly puts anatomist into ROI drawing mode, with a session and some (empty) regions predefined. So you basically just have to click on this pen button in BV, and then just draw in Anatomist, and save (a <ctrl>-S on the toolbox should be enough, the filename is already specified by BrainVisa).
Otherwise, yes, the regions are starting points (corpus callosum is OK).

Denis