Possible bug with defining volume scouts using MNI coordinates

Bugs
1

Hi Francois,

I’ve made a transformation to MNI coordinates in Brainstorm, and selected a point of interest in the posterior left thalamus based on the MNI template. The coordinates in mm are -10 -32 -6. When I enter it into the “set coordinates” box, it goes to a reasonable location in the left posterior thalamus.

I would now like to create a volume scout based on this point, on a mixed model (cortex = surface, subcortical regions = volume). I go to my source model, open with MRI 3D viewer, Atlas > New Atlas > Volume scouts, and then Scout > New coordinates, enter under MNI -10 -32 -6 and grow it enough to see, and it is decidedly in the wrong place.

When I entered the MNI coordinates in the MRI editor, I recorded the MRI coordinates displayed at that time [120 103 124]. I tried a new scout based on those, this time in the ‘MRI coordinates’ option. That’s in a different wrong place.

Should the option of defining scouts by coordinates be working for mixed models? Is there a work-around?

  • Emily
2

Hi Emily,

This option “Scouts > New: Coordinates” was not equipped to work on mixed head models (one of the many combinations of options that are still not handled properly I guess).
I think I fixed it, now it checks properly whether the selected atlas is a volume or surface atlas.
Update Brainstorm and try again.

Francois

3

I confirm that my brain parts are now where I expect them - thanks!