User:Inorton

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Isaiah Norton, Golby Lab, Department of Neurosurgery

contact: inorton @bwh d-t harvard d0t edu

Slicer Notes

Things that aren't fleshed-out enough to go into Mantis, or if I can't fully reproduce yet, can't share the data right now, etc..

Bugs

  • Can't load high-res MEMPRAGE MRI from MGH for AG case in Slicer3. workaround: loaded fine in slicer2, then saved as nrrd. DicomToNRRD also works.
  • CropVolume changes image intensity

Feature Wishes

  • Better transform handling in the reg meta-code: should sort out any hierarchies for cross-registration (ie, want to register to something that is already inside another transform)
  • Put models inside appropriate transform after generation
  • Editing volume inside of transform - don't want to have to move volumes out of transform every time to change labelmaps in a complex scene.
  • Slice intersections in 3D viewer, ie lines/gray/highlight/etc. at the intersection point (helps with depth perception). In Slicer3 this is only supported in 2d widgets.
  • intelligent fiducial picking: for example, jump to nearest local min/max (like spm)
  • option to load nrrd immediately after DicomToNrrd (cli need tweak to add post-handling options?)
  • dynamic (python) module reload
  • debug: to work around MRML scene-load crashes need either 1) cl debug option to output each tag as it is being processed, so that I know which node causes the crash or 2) load prompt for each node in the scene (like the Windows XP selective dll load)

DTI

  • Tract (hyperstreamline) intersection with MR planes (highlighted with color change, ring, etc.)
  • FiberBundle editing!!!

Thoughts

How-to-do-this

  • [LoadBrainPointsIntoSlicer]

Slicer4

Learning Qt

Internal Coding

External links

Other Notes

SuperBuilding Slicer3 on Windows 7

Slicer3 with WrapITK for Python ITK wrapping

Tidbits

UseIntelMKLwithMatlabForFasterSPM

ExternalConnectionsToSPL

LinuxScreenCaptureMovieNotes

CTPhantomSegmentation

LoadAnalyzeIntoBrainLab

LoadfMRIIntoInstaTrak

ImageConversionUtilities