October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow

TODOs

• link the software tools and scripts with the workflow
• prepare a branch in the sandbox with the tools not available in Slicer (confirm with Chris copyright issues)

Software

• Atlas buiding workflow: Slicer 3.5 ~svn r10578. BRAINSFit Slicer extension branch svn r301 (current one is broken). EM Segmenter from 3.4 svn stable branch.

Workflow

Step 1: Prepare the data using the instructions -- LINK

Step 2: Gradient anisotropic diffusion. Tools: Slicer GAD module. Parameters: time step: 0.0625, iterations: 5, conductance: 1.

Step 3: Initial registration 6+9+12 DOF registration. Tools: BRAINSFit svn r301. Parameters: default except CenterOfHead initializer with ROIAUTO sampling region. Comments: failure to recover the pose for Hugo and Valentino (both have severe head tilt in all three planes). Execution time: ~2 min per subject.

Step 4: Manual pose alignment for Hugo and Valentino. Transforms "hardened" in Slicer MRML, volumes saved and re-registered same way as described in Step 3. Registration issue resolved. Tools: Slicer Transforms module, BRAINSFit.

Step 5: Manual ICC for Tommy. Tools: itkSNAP, manual editing by Ginger. Tried Xiaodong's SkullStrippingModule, no luck.

Step 6: Editing of ICC label map. Tools: Slicer smoothing label map module. Parameters: 10 iterations.

Step 7: Manual mask dilation, so that each brain of each subject following registration in Step is contained. Tools: Slicer Editor module. Parameters: 8-neighbor, repeated 3 times.

Step 8: Resampling of the ICC to each subject. Tools: Slicer ResampleVolume2 command line module. Parameters: NN interpolation.

Step 9: Bias field correction with ICC. Tools: Slicer N3MRILightCLI extension. Parameters: default values except number of iterations increased from 50 to 100, convergence threshold decreased from 0.001 to 0.0001, ICC label from Step 8. Execution time: < 2 min per subject. Comments: There are some parameters in N3 which we understand and can play with. Subjective (?) trying to evaluate if the result is better.

Step 10 -- we are here right now: Pipelined registration (6+9+12+BSpline). Tried: (1) ICC ROI from step for moving floating, BSpline step segfaults; (2) ROIAUTO (same as in Step 3), BSpline completes, but resampled volume does not make any sense. AF: I suspect BSpline registration may not be able to handle non-axis-aligned volumes. Comments: When resampling, do not forget to use higher order interpolator.

Step 11: Average all subjects to get average template.

Step 12: Manually edit ICC labels for each subject, skull strip here or after Step 9, edit and repeat all steps to improve registration.

Remaining steps:

• Segment GM/WM/CSF+Putamen/Caudate/Hippocampus in the averaged template.
• Invert the deformation field from Step 10 (Step 12?), and map the segmentations to the individual subjects.
• Manually edit each subject labels. Map back to the average template and calculate the probabilities atlas.
• Run EM Segmenter to get the bias field. Repeat again?