I want to implement structural connectivity on 17 predefined ROIs in MNI coordination with a sphere radius of 8. Furthermore, these are my ROIS and their MNI coordination.
I wanted to know what should I do, is it available in Mrtrix, and what are the commands?
before this approach, I obtained structural connectivity based on AAL atlas regions. I have done all steps until sift command.
Thanks in advance
There are two separate steps that need to be done here:
- Definition of a sphere of radius 8mm
- Transformation of that sphere from MNI space to subject space
I see two ways of possibly doing this:
Using an actual sphere
- Transform ROI centroid from MNI space to subject space
This would involve interpolating the subject-to-MNI warp field at each ROI centroid to determine an appropriate centroid location in subject space. This may involve a little coding or manual intervention, but is not an overly complex operation.
- Impose a spherical ROI of 8mm radius in subject space
The input to the
tckedit -include option can be a comma-separated list of 4 values, being the X, Y, Z and radius of a sphere.
Drawing a sphere and transforming it
- Use the
mredit -sphere option to draw binary mask images in template space, each containing a sphere of fixed radius around each ROI centroid.
- Transform each of those images from template to subject space (e.g.
The results will be fractionally different between the two, but either should function well enough.