MRITOTAL Spatial Normalization of Population Average Landmark Surface-based (PALS) Atlas Fiducial Surfaces

2004-11-02, Donna Hanlon, Van Essen Lab

Normalize structural volume using MRITOTAL

A shell script was used to invoke the following commands on each case:

3dAFNItoMINC Human_Buckner_Case1+orig.HEAD
mritotal Human_Buckner_Case1.mnc Human_Buckner_Case1.xfm
mincresample -transformation Human_Buckner_Case1.xfm \
	-like average_305_mask_1mm.mnc \
	Human_Buckner_Case1.mnc mni_Human_Buckner_Case1.mnc

Apply the affine matrix to the coordinate files using AFNI's Vecwarp

Stripping the node numbers and comments and applying the matrix directly to the triplets works fine, but converting to full-brain grid; applying the matrix; and translating -90,-126,-72 results in an offset between the volume and surface.

  1. Prepare the mritotal output xfm for input to AFNI's Vecwarp:
    tail -3 Human_Buckner_Case1.xfm > Human_Buckner_Case1.mni_mat
    echo "0 0 0 1" >> Human_Buckner_Case1.mni_mat
  2. Write coord header to output file:
    head -12 Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.73730.coord > Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.coord
  3. Strip header and node numbers from coord file, and apply mritotal matrix output to stripped coordinates:
    tail +13 Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.73730.coord | cut -f2-4 -d' ' | Vecwarp -matvec Human_Buckner_Case1.mni_mat > Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.triplets
  4. Insert node numbers into Vecwarp output and append to output file:
    triple_to_coord Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.triplets >> Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.coord

Make sure warped surface and MRITOTAL-normalized volume align perfectly

  1. Use a text editor to create a spec file like this:
    CLOSEDtopo_file Human.sphere_6.LEFT_HEM.73730.topo
    FIDUCIALcoord_file Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_MRITOTAL.73730.coord
  2. Start caret5 and load all files in this spec file.
  3. File: Import file: Minc: mni_Human_Buckner_Case1.mnc
  4. Switch view to VOLUME; press D/C and select Overlay/Underlay - Volume.
  5. Toggle on the Show surface contour checkbox in the lower right of the menu.
  6. Switch between Horizontal, Parasagittal, and Coronal views, scrolling up and down through the volume, to make sure that the contour aligns perfectly with the mni_Human_Buckner_Case1.mnc volume.