Documentation/Labs/DeprecatedModules

This page is here to capture the list of modules we would like to bundle into a Slicer extension named "DeprecatedModules".

Action plan

All these modules would be added to their own git repository:

• History should be extracted and conserved.
• Data should be added to Midas.

Then, two approaches:

1) A git repository named "DeprecatedModulesExtension" could combine them using the "git submodule" approach".

2) The concept of meta extension could be introduced (similar to what is down with apt-get), the extension would appear in the catalog and would simply allow to install all its dependent extensions.

Jc: Approach 2 is preferred.

Modules

I propose to include all the module belonging to the CLI "Legacy" category: See also http://www.slicer.org/slicerWiki/index.php/Developer_Meetings/20130226#Listing_of_Modules

• AffineRegistration (it's just a simple registration example, BRAINS registration provides all its functionality) Removed in r23599
• BSplineDeformableRegistration (it's just a simple registration example, BRAINS registration provides all its functionality) Removed in r23599
• LinearRegistration (it's just a simple registration example, BRAINS registration provides all its functionality) Removed in r23599
• MultiResolutionAffineRegistration Removed in r23599
• OtsuThresholdImageFilter Removed in r23599
• OtsuThresholdSegmentation Removed in r23599
• ResampleScalarVolume => Essential feature (typically high-resolution data is downsampled with this filter to conserve memory and increase execution speed; e.g., for registration), don't remove without replacement (or at least don't put it in an extension that collects useless modules only)
• RigidRegistration (it's just a simple registration example, BRAINS registration provides all its functionality) Removed in r23599
• MRIBiasFieldCorrection => Essential feature for MRI registration, don't remove without replacement (or at least don't put it in an extension that collects useless modules only) Removed in r23599. Jc: Checking with Hans and Steve what it would take to port to module to ITKv4
  • There is this module that is more up to date and arguable is more easy to use: http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/N4ITKBiasFieldCorrection. This module remains in the main application.
• MIDASApplications Removed in r23396
• BatchMakeApplications Removed in r23396

The following module will be maintained around:

• BSplineToDeformationField => Needed by EMSegment; very useful in general, as the BSpline transform is not usable by external programs, but the conversion result (deformation field) can be processed and visualized in ParaView etc.
• ExpertAutomatedRegistration => Needed by TubeTK. - Can it be replaced by BRAINS?
• FiducialRegistration => Replaced by Landmark Registration module and Fiducial Registration Wizard (in SlicerIGT extension)? Therefore, probably not used anymore?. It turns out that currently the one provided by SlicerIGT does not work on MacOSX. Following Dominik comment, we will keep the module around. See [here https://github.com/Slicer/Slicer/pull/169#issuecomment-52830418]

The following module are built but not installed:

• TestGridTransformRegistration
• DiffusionTensorTest

Links

Mailing list thread: http://slicer-devel.65872.n3.nabble.com/Listing-of-Modules-in-Slicer-tp4027711p4027723.html

Issues

• http://na-mic.org/Mantis/view.php?id=3401