Difference between revisions of "October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow"
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== Workflow == | == Workflow == | ||
| − | + | Re-work for Gucci as template subject. | |
| − | '''Step | + | '''Step 1 -- DONE''': Prepare the data using the instructions -- LINK |
| − | '''Step | + | '''Step 2 -- DONE''': Gradient anisotropic diffusion. Tools: Slicer GAD module. Parameters: time step: 0.0625, iterations: 5, conductance: 1. ''Note: Should try with and without GAD. Sandy suggested GAD can cause troubles for EM.'' |
| − | '''Step | + | '''Step 3 -- AF''': 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 5''': Manual ICC for Tommy. Tools: itkSNAP, manual editing by Ginger. Tried Xiaodong's SkullStrippingModule, no luck. | + | '''Step 4 -- AF''': 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 -- Ginger''': 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 6''': Editing of ICC label map. Tools: Slicer smoothing label map module. Parameters: 10 iterations. | ||
| Line 26: | Line 28: | ||
'''Step 8''': Resampling of the ICC to each subject. Tools: Slicer ResampleVolume2 command line module. Parameters: NN interpolation. | '''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 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. ''Note: should also try not correcting for bias field outside EM.'' |
'''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. Debugging data: [[File:Tommy-Calvin-bspline_registration.tgz]] | '''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. Debugging data: [[File:Tommy-Calvin-bspline_registration.tgz]] | ||
Revision as of 14:56, 12 October 2009
Home < October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflowTODOs
- 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
Re-work for Gucci as template subject.
Step 1 -- DONE: Prepare the data using the instructions -- LINK
Step 2 -- DONE: Gradient anisotropic diffusion. Tools: Slicer GAD module. Parameters: time step: 0.0625, iterations: 5, conductance: 1. Note: Should try with and without GAD. Sandy suggested GAD can cause troubles for EM.
Step 3 -- AF: 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 -- AF: 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 -- Ginger: 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. Note: should also try not correcting for bias field outside EM.
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. Debugging data: File:Tommy-Calvin-bspline registration.tgz
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?
