Custom seed mask from anatomical atlas


I am interested in tracking fibers coming out of the GMWM interface of a particular functional region, let’s say visual cortex. I can access such an atlas (e.g. Juelich atlas) from FSLEyes and export a mask. However, mask is correct only with standard MNI152 overlay. My scans are in different orientations so using a mask straight away will be incorrect. I am assuming such an approach shall be fine?

  1. Use flirt to get transform between my T1 (coregistered to DWI) and atlays overlay (MNI152_1mm_brain)
  2. Use inverse transform on mask so that mask is showing functional region on my T1
  3. Derive WMGM mask from T1 / T2
  4. Overlap functional mask with WMGM mask
  5. Mask from pt. 4 is a set of seed points for tracking.

Or shall I do something else?

Kind regards,