Predefined ROIS connectivity

1

Hi guys!
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.
ROIS

Thanks in advance

2

Hi Fateme,

There are two separate steps that need to be done here:

  1. Definition of a sphere of radius 8mm
  2. Transformation of that sphere from MNI space to subject space

I see two ways of possibly doing this:

Using an actual sphere

  1. 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.
  2. 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

  1. Use the mredit -sphere option to draw binary mask images in template space, each containing a sphere of fixed radius around each ROI centroid.
  2. Transform each of those images from template to subject space (e.g. mrtransform).

The results will be fractionally different between the two, but either should function well enough.

Cheers
Rob