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.
- Start matlab; enter spm at prompt.
- Select fMRI Time Series.
- Select Defaults: Spatial Normalization: Writing Normalized: Template bounding box.
- Select Defaults: Spatial Normalization: Writing Normalized: Voxel size 1 1 1.
- Select Normalize: Determine parameters and write normalized.
- Enter 1 for number of subjects and pres the return key.
- When prompted for the image to determine parameters, change the filter from .img to .mnc, and select Human_Buckner_Case1.mnc.
- When prompted for the image to write normalized, select Human_Buckner_Case1.mnc.
- When prompted for the template/target, change the filter back to .img and select T1.img.
- Select Bilinear for the interpolate method.
- After the normalization completes, Toolbox: Deformations.
- From the Deformations menu, select Deformations from sn3d.mat.
- Select Human_Buckner_Case1_sn.mat.
- When the SPM menu becomes responsive, select Toolbox: Deformations again to make the Deformations menu active.
- Select Deformations: Invert Deformations.
- Enter 1 for number of subjects and pres the return key.
- Select deformation field files y1_Human_Buckner_Case1.img, y2_Human_Buckner_Case1.img, and y3_Human_Buckner_Case1.img.
- For Image to base inverse on, change the filter from *.img to *.mnc and select Human_Buckner_Case1.mnc.
- When the SPM menu becomes responsive, look for iy1_Human_Buckner_Case1.img, iy2_Human_Buckner_Case1.img, and iy3_Human_Buckner_Case1.img.
- Press the Quit button to exit SPM.
- Type "quit" at the Matlab prompt to exit Matlab.
Apply the inverse deformation to the coordinate files
- 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
- Start caret5 and load all files in this spec file.
- Select Surface: Transform: Apply SPM Inverse Transform.
- Select normalized volume: nHuman_Buckner_Case1.hdr.
- Select Inverse X volume: iy1_Human_Buckner_Case1.img.
- Select Inverse Y volume: iy2_Human_Buckner_Case1.img.
- Select Inverse Z volume: iy3_Human_Buckner_Case1.img.
- Press Apply and wait for the deformation to apply.
- Select Surface: Transform: Translate: -90,-126,-72
- Select File: Save Data File: Coord file: Human_Buck_Case1.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM99.73730.coord
- Switch view to VOLUME; press D/C and select Overlay/Underlay - Volume.
- Toggle on the Show surface contour checkbox in the lower right of the menu.
- 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.