Osirix v5.6

Straighten spinal cord

  1. Load image
  2. select 3D curved MPR
  3. select the top left icon with the green curved line and red spots
  4. select a couple of points along the spinal cord
  5. select … view and select export this image to a DICOM file (cmd+e)
    1. select a series with the following settings
    2. select transverse slices

Manual segmentation of the spinal cord

  1. Load image
  2. Select axial orientation (easier to have both views on screen)
  3. Disable interpolation for zoom. Menu Osirix → Preferences → Viewer → Miscellaneous → Check No interpolation for zoom
  4. Select ROI tool (icon… not ROI menu) → Closed polygon
  5. Create a 2D segmentation of the spinal cord at each vertebral level (save ROIs to extract cross-sectional area)
  6. Select ROI → ROI Volume → Generate missing ROIs (save ROIs)
  7. Select ROI → Set pixels values to :
    1. Apply to All ROIs
    2. Set pixels that are Inside ROIs
    3. If current value is larger than 0 and if current value is smaller than 10000 (check boxes)
    4. To thus new value : 1
    5. Click “OK”
  8. Apply same process to outside ROIs pixels and change value to 0
  9. Set the image dynamic (WL/WW –> “Set WL/WW manually) to 0 and 1
  10. Right click and export to DICOM file(s)
    1. All images of the series
    2. Image format : as stored in memory in 16-bit BW (important to keep dimensions!)
    3. Change name and click “OK”

Use dcm2nii to transform DICOM files to a Nifti image.


Sometimes, OsiriX change dimensions and orientation… To repair this problem, you must use c3d. If it's just a orientation problem, you may use sct_orientation.

Usage :

  1. c3d <targetfilename> <inputfilename> -reslice-identity -o <outputfilename>
  2. sct_orientation -i <inputfilename> -o <outputfilename> -orientation <three letter code of target orientation>