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

2004-10-08, Donna Hanlon, Van Essen Lab

Create +acpc.HEAD and +tlrc.HEAD files for volume

See the AFNI manual or online documentation. I used AFNI Version 2.55d of 08 Aug 2003 to do the normalization. (This is pretty old, because my wget.sh script was calling the linux_glibc21 version, which I think Cox, et al, stopped supporting. Also, I'm a little afraid to upgrade, because I'm afraid they might get rid of 3dANALYZEtoAFNI, which I still use and value.)

Apply the talairach warp to the coordinate files using AFNI's Vecwarp

Because the VE lab used to map vtk files in "native" space, Bob Cox wrote Vecwarp to output coord files that way. So we have to shift the coord files from AC-origin to "full brain grid" (i.e., origin is left-most dataset corner, posterior-most dataset corner, inferior-most dataset corner); apply the +tlrc warp; and then shift the coords back to AC-origin.

  1. Use text editor to create a Human_Buck_Case1.matrix file like this, where the numbers in the right-most column are the AC coordinates in the *LR*params file (i.e., AC[xyz]_WholeVolume):
    1 0 0 88
    0 1 0 123
    0 0 1 74
    
  2. Use text editor to create a tlrc.matrix file like this:
    1 0 0 -80
    0 1 0 -110
    0 0 1 -65
    
  3. Vecwarp -matvec Human_Buck_Case1.matrix -input Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_711-2C.73730.coord > case1.L.fbg
  4. Vecwarp -apar Human_Buckner_Case1+tlrc.HEAD -input case1.L.fbg > case1.L.warp
  5. Vecwarp -matvec tlrc.matrix -input case1.L.warp > Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_AFNI.73730.coord

Make sure warped surface and +tlrc volume align perfectly

Note: Caret can't warp volumes to +acpc or +tlrc the way AFNI can; therefore, we need to write a +tlrc.BRIK for Caret to view.

  1. Start AFNI, and make sure Human_Buckner_Case1 is the selected anatomy.
  2. Switch to +tlrc view.
  3. Define Datamode: Write Anat to write a +tlrc.BRIK, which Caret needs to view the volume.
  4. Quit AFNI.
  5. 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_AFNI.73730.coord
    volume_anatomy_file Human_Buckner_Case1+tlrc.HEAD
    
  6. Start caret5 and load all files in this spec file.
  7. Switch view to VOLUME; press D/C and select Overlay/Underlay - Volume.
  8. Toggle on the Show surface contour checkbox in the lower right of the menu.
  9. Switch between Horizontal, Parasagittal, and Coronal views, scrolling up and down through the volume, to make sure that the contour aligns perfectly with the wHuman_Buckner_Case1.hdr volume.