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Linear Transforms

Warning

Ensure you are using 3D Slicer 4.10.2:
Windows (x64): http://slicer.kitware.com/midas3/item/433684
Mac OS X: http://slicer.kitware.com/midas3/item/433773
Linux: http://slicer.kitware.com/midas3/item/435293

Naming Scheme for Fiducial Files

  • [VolumeID]_[Contrast]_[Rater]_[N] (e.g. macaqueMNI_T1_JL_01)

  • [VolumeID] = the identifier for the volume on which you are performing the fiducial placements (see specific protocol for naming)

  • [Contrast] = T1 (all templates are currently T1)
  • [Rater] = the unique identifier for the rater performing the fiducial placement; convention will be first initial and last name to prevent overlap
  • [N] = reference for fiducial placement session (helpful if performing placements more than once; starting with 1)

AC-PC Placement

Download assigned volume/template from github repository. Go to Markups Module and create markups list entitled ACPC_[VolumeID]_[Contrast]_[Rater]_[N]. Place AC and PC landmarks:

  1. AC = anterior commissure (center)
  2. PC = posterior commissure (center)

Create new AC-PC transform

Create a new markups list entitled Fid32_[VolumeID]_[Contrast]_[Rater]_[N]. Create a new markups list entitled midline.

To create a new AC-PC Transform you must place AC and PC fiducial markers in previous step.

  1. Copy AC and PC markers from ACPC to the midline markups list.
  2. Go back to the midline markups list and place a fiducial marker in the infracollicular sulcus (point 3)
  3. Place another fiducial marker at the Genu of CC (point 19)
  4. You should now have AC and PC in the ACPC markups list and AC, PC, infracollicular sulcus and Genu of CC in the midline markups list
  5. Under modules select Registration → Specialized → ACPC Transform.
  6. In the Transform Panel, under ACPC Line select the ACPC markups list, under Midline select the midline markups list, and under Output transform select "Create new linear transform as…" and name it Output transform.
  7. Click apply at the bottom of the window.
  8. Note: if the volume turns off → under modules go to Data. Beside the image volume select the ‘eye’ icon to turn the volume back on.
  9. Next under Modules go to Transforms and under Active Transform dropdown tab select the transform you created in step 6 (if not already selected).
  10. Under Apply Transform select all 4 items (i.e macaqueMNI, ACPC_macaqueMNI_T1_GG_0l, midline, and Fid32_macaqueMNI_T1_GG_0l) and transfer them to the transformed side.