SPM99 Spatial Normalization of Population Average Landmark Surface-based (PALS) Atlas Fiducial Surfaces

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

Normalize volume and invert deformation field in SPM

Note: These procedures require the update that allows SPM99 to read Minc files, as well as the Deformation toolbox.

  1. Start matlab; enter spm at prompt.
  2. Select fMRI Time Series.
  3. Select Defaults: Spatial Normalization: Writing Normalized: Template bounding box.
  4. Select Defaults: Spatial Normalization: Writing Normalized: Voxel size 1 1 1.
  5. Select Normalize: Determine parameters and write normalized.
  6. Enter 1 for number of subjects and pres the return key.
  7. When prompted for the image to determine parameters, change the filter from .img to .mnc, and select Human_Buckner_Case1.mnc.
  8. When prompted for the image to write normalized, select Human_Buckner_Case1.mnc.
  9. When prompted for the template/target, change the filter back to .img and select T1.img.
  10. Select Bilinear for the interpolate method.
  11. After the normalization completes, Toolbox: Deformations.
  12. From the Deformations menu, select Deformations from sn3d.mat.
  13. Select Human_Buckner_Case1_sn.mat.
  14. When the SPM menu becomes responsive, select Toolbox: Deformations again to make the Deformations menu active.
  15. Select Deformations: Invert Deformations.
  16. Enter 1 for number of subjects and pres the return key.
  17. Select deformation field files y1_Human_Buckner_Case1.img, y2_Human_Buckner_Case1.img, and y3_Human_Buckner_Case1.img.
  18. For Image to base inverse on, change the filter from *.img to *.mnc and select Human_Buckner_Case1.mnc.
  19. When the SPM menu becomes responsive, look for iy1_Human_Buckner_Case1.img, iy2_Human_Buckner_Case1.img, and iy3_Human_Buckner_Case1.img.
  20. Press the Quit button to exit SPM.
  21. Type "quit" at the Matlab prompt to exit Matlab.

Apply the inverse deformation to the coordinate files

  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_711-2C.73730.coord
    volume_anatomy_file nHuman_Buckner_Case1.hdr
    
  2. Start caret5 and load all files in this spec file.
  3. Select Surface: Transform: Apply SPM Inverse Transform.
  4. Select normalized volume: nHuman_Buckner_Case1.hdr.
  5. Select Inverse X volume: iy1_Human_Buckner_Case1.img.
  6. Select Inverse Y volume: iy2_Human_Buckner_Case1.img.
  7. Select Inverse Z volume: iy3_Human_Buckner_Case1.img.
  8. Press Apply and wait for the deformation to apply.
  9. Select Surface: Transform: Translate: -90,-126,-72
  10. Select File: Save Data File: Coord file: Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM99.73730.coord
  11. Switch view to VOLUME; press D/C and select Overlay/Underlay - Volume.
  12. Toggle on the Show surface contour checkbox in the lower right of the menu.
  13. 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.