pub:fmri:paraview_convert_3d [NTU IMRL]
 

ParaView + Convert 3D

Convert Analyze / NIFTI files to vtk 3D files

Install ITK-SNAP

  • Download ITK-SNAP VERSION 2.0 here and install.

Use ITK-SNAP

  • for windows users
    • Double click problem ⇒ ITK-SNAP 2.0 ⇒ ITK-SNAP
    • or directly run itksnap-2.0.0-win32-x86.exe in the installed folder.
  • Open your fMRI Analyze / NIFTI file.
    • File ⇒ Open Greyscale Image
    • Select your file
    • Confirm Image file format
    • Next ⇒ Confirm the parameters ⇒ Finish
  • Check the output orientation
    • Tools ⇒ Reorient Image…
    • The orientation using in paraview is LPI
      • RPI
        • default ANALYZE orientation
        • SPM2, SPM99
        • 1000 Functional Connectomes Project
      • LPI
        • Talairach template coordinate system
        • MNI template coordinate system
        • Default ParaView load
        • IBASPM template coordinate system

  • Convert to vtk 3D file.
    • File ⇒ Save ⇒ Greyscale Image
    • Use VTK File as file format ⇒ Save

Install ParaView

  • Download ParaView here and install.

Use ParaView

  • for windows users
    • Double click problem ⇒ ParaView-3.8.0 ⇒ ParaView

Build slice background

  • FileOpen
  • Click avg152T1.vtk in Pipeline Browser and click Apply in Object Inspector
  • FilterCommonCalculator
    • Fill scalars in the column under the Result Array Name
      • for using different colormaps in this 3D model
    • click Apply
  • FilterCommonSlice ⇒ click X NormalApply
  • Click Slice1, rename to slice_x
  • Object Inspector ⇒ DisplayEdit Color MapChoose Preset ⇒ select Grayscale ⇒ Ok
  • Repeat the steps to add more slices

Build glass brain

  • FileOpen
  • Apply
  • FilterCommonContour ⇒ edit value Range to 0.5(or other range, try some values) ⇒ Apply
    • Object Inspector ⇒ DisplayStyle ⇒ change to Wireframe
      • Set Opacity to 0.02
      • Color by ⇒ Solid Color
      • Set Ambient Color…

Build activation area

  • FileOpen
    • Select your activation vtk file.(build from standard FSL or SPM files using ITK-SNAP)
  • Apply
  • FilterCommonThreshold ⇒ edit threshold Range ⇒ Apply
  • Object Inspector ⇒ Display ⇒ Change color
  • [Optional] Change Representation to volume
  • [Optional] Add filterAlphabeticalExtractSurface ⇒ Add filterAlphabeticalSmooth⇒ Number of Iterations = 500

References

ParaView

 
pub/fmri/paraview_convert_3d.txt · Last modified: 2010/06/29 12:13 by gobidesert     Back to top