Developer Meetings/20131008

Update documentation

• Ron's priorities for final year of NAMIC funding

Not yet done

1. Update the slicer user documentation pages by RSNA. Describe up-to-date workflows in the examples. Make sure all the features are described. Make sure authors, institutions, and grants are properly acknowledged. The following is an incomplete list:
   1. Probe Volume With Model SurfaceToolbox (Luca Antiga)
   2. ACPC Transform (Nicole Aucoin)
   3. Cast Scalar Volume (Nicole Aucoin)
   4. Colors (Nicole Aucoin)
   5. LUTs (Nicole Aucoin)
   6. Mask Scalar Volume (Nicole Aucoin)
   7. Merge Models (Nicole Aucoin)
   8. Model Maker (Nicole Aucoin)
   9. Models (Nicole Aucoin)
   10. Model To LabelMap (Nicole Aucoin)
   11. PET Standard Uptake Value Computation (Nicole Aucoin)
   12. Threshold Scalar Volume (Nicole Aucoin)
   13. Fiducial Registration (Stephen Aylward)
   14. Gaussian Blur Image Filter (Stephen Aylward)
   15. Resample Scalar/Vector/DWI Volume (Francois Budin)
   16. Crop Volume (Andrey Fedorov)
   17. Intensity Difference Metric (Andrey Fedorov)
   18. N4ITK Bias Field Correction (Andrey Fedorov)
   19. Data (Julien Finet)
   20. Models (Julien Finet)
   21. Robust Statistics Segmenter (Yi Gao)
   22. Segmentation Aided Registration (Yi Gao)
   23. Reformat (Michael Jeulin-Lagarrigue)
   24. Demon Registration (BRAINS) (Hans Johnson)
   25. Foreground Masking (BRAINS) (Hans Johnson)
   26. General Brainsfit Registration (Hans Johnson)
   27. Resample Image (BRAINS) (Hans Johnson)
   28. Vector Demon Registration (Hans Johnson)
   29. KSlice Interactive Segmenter (Ivan Kolesov)
   30. Simple Filters (Bradley Lowekamp)
   31. WatershedFromMarkers (Bradley Lowekamp)
   32. SNR Measurement (Babak Matinfar)
   33. Main window (JC)
   34. Welcome to Slicer (JC)
   35. Add Scalar Volumes (Jim Miller)
   36. CheckerBoard Filter (Jim Miller)
   37. Create DICOM Series (Jim Miller)
   38. Curvature Anisotropic Diffusion (Jim Miller)
   39. Dicom to Nrrd Converter (Jim Miller)
   40. Extract Skeleton (Jim Miller)
   41. Gradient Anisotropic Diffusion (Jim Miller)
   42. Grayscale Fill Hole Image Filter (Jim Miller)
   43. Grayscale Grind Peak Image Filter (Jim Miller)
   44. Grayscale Model Maker (Jim Miller)
   45. Histogram Matching (Jim Miller)
   46. Median Image Filter (Jim Miller)
   47. Multiply Scalar Volumes (Jim Miller)
   48. Orient Scalar Volume (Jim Miller)
   49. Simple Region Growing Segmentation (Jim Miller)
   50. Subtract Scalar Volumes (Jim Miller)
   51. View Controllers (Jim Miller)
   52. Voting Binary Hole Filling Image Filter (Jim Miller)
   53. Label Map Smoothing (Dirk Padfield)
   54. Data Probe (Steve Pieper)
   55. DICOM (Steve Pieper)
   56. Editor (Steve Pieper)
   57. Endoscopy (Steve Pieper)
   58. Fiber Bundle to Label Map (Steve Pieper)
   59. Label Statistics (Steve Pieper)
   60. .mrb (Steve Pieper)
   61. Sample Data (Steve Pieper)
   62. Vector to Scalar Volume (Steve Pieper)
   63. Volumes (Steve Pieper)
   64. EMSegment Command-line (Kilian Pohl)
   65. EMSegment Easy (no atlas) (Kilian Pohl)
   66. EMSegment (with atlas) (Kilian Pohl)
   67. DTIExport (Sonia Pujol)
   68. DTIImport (Sonia Pujol)
   69. OpenIGTLink IF (Junichi Tokuda)
   70. Diffusion Tensor Scalar Measurements (Demian Wasserman)
   71. Diffusion Weighted Volume Masking (Demian Wasserman)
   72. DWI Joint Rician LMMSE Image Filter (Demian Wasserman)
   73. DWI Rician LMMSE Filter (Demian Wasserman)
   74. DWI To DTI Estimation (Demian Wasserman)
   75. DWI to Full Brain Tractography (Demian Wasserman)
   76. Resample DTI Volume (Demian Wasserman)
   77. Tractography Label Map Seeding (Demian Wasserman)
   78. Image Label Combine (Alex Yarmarkovich)
   79. Sceneviews (Alex Yarmarkovich)
   80. Tractography Interactive Seeding (Alex Yarmarkovich)
   81. Transforms (Alex Yarmarkovich)
   82. Left Atrial Scar Segmenter (LiangJia Zhu)
   83. Left Atrium Segmenter (LiangJia Zhu)

Recently updated Module Documentations

1. 1. Annotations (Nicole Aucoin) 12:11, 24 September 2013.
   2. Markups (Nicole Aucoin) 11:59, 24 September 2013.
   3. Volume rendering (including label data sets) (Julien Finet) 11:43, 19 September 2013.
   4. Introduction to Registration (Dominik Meier) 16:18, 13 September 2013.
   5. Tractography Display (Demian Wasserman) 12:26, 13 September 2013. by Alex Yarmarkovich
   6. FiberBundleLabelSelect (Alex Yarmarkovich) 11:33, 13 September 2013.

Other improvements

1. 1. when I save an MRB repeatedly, my customizations from last time should be remembered. Right now, the save module forgets that I selected .mrb for my last save. I need to tell it again. When doing so, the default name turns into .mrb.mrb. It also forgets that I pointed it to a particular directory and offers to save in the default location. Having this persist for the session only would be good. If persistent across session, a reset button would be good.
   2. the location from which something was loaded should be the default for saving.
   3. create a preset w/l+LUT in the volume module (scaled from 0 to 1), and corresponding transfer function for FA maps in the volume rendering module (bug #1857)
   4. on/off switch in the editor module for volume rendering of active label map
2. All tutorials should be updated, including new basic features such as .drag and drop and .mrb
3. Unable to use Volume module Threshold widget in a meaningful way
4. Better presentation of text in sceneviews

1. Review critical bugs / Open questions

• Nonlinear transform support (Alex)
  • Resampled on the fly
  • Pre-cached non-linear hardened version
  • Need to fix read/write of grid transforms
  • Fix resample CLIs to consistently accept grid transforms
  • See: http://www.na-mic.org/Wiki/index.php/Handling_deformable_transforms_in_Slicer_meeting_minutes
• Migrating Rulers into Markups module (Nicole)
• Pluggable registration module (Steve, for Head and Neck Radiotherapy DBP)
• Each DBP to be pinged for wish list by Engineering contact
  • Steve -> Greg
  • Jim -> Rob/Josh
  • Stephen -> Jack
  • Dan -> Hans
• Steve will send blanket email to all DBPs requesting their priorities
• In coming months we will finalize a strategy for 4.x releases as final NA-MIC deliverables