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Medical-imaging-processing-software.md

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Practice on medical imaging processing software

Table of contents

Medical Image Analysis Using FIJI software

  • open/import a specific file in different formats
  • zoom in/out an image: +/- key
  • browse a slice: left/right key
  • see 3D image in 3 directions
    • stacks->orthogonal views
    • stacks->reslice '/' key
  • compute mean/std value: 'm' key
    • results/analyse->set measurements
    • the whole slice
    • the selected area
  • Image->Lookup Tables, set different show ways
  • Analyse->Plot profile, make a plot of selected area
  • Image->Stacks->Statistics, statistics of a image
  • Image->Show Info, save image info to a file
  • Color bar: Analyze > Tools > Calibration Bar
  • View 3D imagein 3 directions: Ctrl+Shift+H
  • Image > Stacks > Make Montage: show all slices in a table
  • Image > Stacks > Images to Stack: make multiple images into a stack
  • Image > Stacks > Z Project (Max intensity): make all the max value of slices into one slice
  • Image > Stacks > Z Project (Average intensity): make all the average value of slices into one slice
  • Image > Stacks > Z Project (Sum slices): make all the slices into one slice
  • Process > Enhance Contrast: show pet image more clearly
  • Image > Overlay: add another image on the current image
  • Export GIF: Image > Stacks > 3D Project, then click File > Save as > GIF
  • Copy a ROI (line or square) to another window, select Analize > Tools > ROI manager, add current ROI, then on another window, select 'show all' from ROI manager

Medical Image Analysis Using Slicer software

  • generate a gif
    • Modules-> Utilities->ScreenCapture
    • Output type: video, image series, lightbox image
  • show : click left-up corner buttons on three views respectively
  • Color bar: Volume > Color Legend. Or right-click the image to show the color legent
  • Overlay: Left upper corner of show panel > F > B
  • MIP: Lookup tables > PET-Maximum Intensity Projection
  • Isodose: In radiotherapy, set threshold value of each line
  • Adjust image contrast by right-clicking 'Adjust window/level'

Medical Image Analysis Using ITK-SNAP software

  • It is easy to open a CT and PET image in one window or both two windows, the position is the same.
  • Adjust the contrast by clicking auto mode.
  • Load segmentation masks on the CT images and segmentation organs in 3D mode.
  • When mask and CT are loaded, the left side will show CT value and mask value of a point.
  • PaintBrush Mode on masks->Right click, remove label; Left click, add label.
  • Polygon Mode -> Draw line on current label -> accept -> move to next slide -> paste last polygon -> drag the line to fine tune.
  • LabelEditor -> Hide certain labels in all windows to only show one label.
  • LabelEditor -> Actions -> Import/Export Label Descriptions.
  • Export dcm data to nii.gz file