[Mristudio-users] Landmarker

[susumu]

Hi Darshan,

1) You need to save the tracking results as the "binary" image, which save
the data as 1/0 map with the dimensions same as the original data. The
pixels that contain the tract becomes 1 and everything else is 0. You can
transform this 3D map in the same way you transform images. Of course, you
can not directly normalize this 1/0 map, because it doesn't look like a
brain. So, you need to use an anatomical image, like b0, for the
transformation, and apply the transformation to this 1/0 map. 

2) it is difficult to know exactly which problem you had, but in general,
here are the things you need to know.

> Both the atlas and your data must have the same number of landmarks placed
on the corresponding structures.
> You need a certain number of landmarks distributed in 3D space to run 3D
normalization. For example, if you place only 3 landmarks in one 2D plane
and try to run 3D normalization, you get an error

3) No there is no meaning in the order of landmarks. However, each landmark
in the template and your data have to be placed in the corresponding
locations and order. For example, if you place landmarks at the cerebral
peduncle (#1), internal capsule (#2), and cingulum (#3) in the template and
place them in the order of the cerebral peduncle - cingulum - internal
capsule in the subject brain, it won't do the correct transformation.

Hope this will help.

Susumu