Common Functions Used by Brain Mappers in BIC-MNI Display

Most functions in Display are accessible either from the clickable, keyboard pop-up menu or the typing the corresponding key on the actual keyboard. The key will be indicated in square brackets (e.g. [Key]) in this documentation.

  1. Load MRI and PET Images
  2. From a terminal/console window:

    $> Display directory/path/if/required/mri_file.mnc path/if/req/pet_file1.mnc path/if/req/pet_file2.mnc ...  
    

    Recommended placement of Display windows

    Also, I recommend closing any unnecessary windows and minimizing all other applications so that the 4-panel window can be viewed with no other layers above or below it. When using the "Save Slice Image" option, it seems that everything in the panel (including bits from other windows) of interest gets saved.

    If the system can't find the file you've indicated, or if there is a problem with the file, you should get an error message in the terminal window:

  3. Toggle Volume of Interest
  4. To change the settings of

    From the Main menu, select "Slice View" [S], then Current Volume [T] and keep pressing [T] until the image you want becomes active. When it is, the colour bar (left hand side) and the title bar (top) of the 4-panel window will display the appropriate colour scheme and filename.

  5. Adjust an image's colour coding
  6. Pop to Main menu [space], Select Colour Coding [D], Select desired colour scheme:

  7. Adjust Over/Under Colour
  8. In the Colour Coding Menu, select Overcolour [X] and type "transparent" at the prompt in the terminal window. Then, select Undercolour [Z] and type "transparent" at the prompt in the terminal window.

    Although tab-completion does not work in the Display terminal window, you can use the mouse to highlight (select with left mouse button) and paste (click middle mouse button) text in the terminal window.

  9. Adjust Range of Displayed Colour Map
  10. Use sliders on colour bar or, from the Colour Coding Menu, select Range [H] and type in the lower and upper limits at the prompt in the terminal window.

  11. Navigate the Volume
  12. Adjust Slice Size Within a Panel
  13. Move Slice Window Within a Panel
  14. Adjust Opacity of Activation Image
  15. Turn Cursor On or Off
  16. Pop to the Main menu [space], choose Segmenting [F], Cursor Vis On/Off [4]

  17. Save image of slice of interest
  18. Pop to the Main menu [space], select File [T]. Put the mouse arrow over the slice of interest and type from the keyboard [S]. Type in a meaningful file name at the prompt in the terminal window. The file is saved in .rgb format; it will be useful if you use that extension as part of the filename.

  19. Open image of slice
  20. Use imgview or imgworks, from another terminal window.

    $> imgworks meaningful_filename.rgb
    

    The program imgworks allows you to crop the image and perform other manipulations. If you double-click the image file from the "Finder" it will open with imgview.

  21. Save image in another file format
  22. Both imgview and imgworks allow you to save in various popular file formats (.gif, .tiff, etc.). Imgview seems to have more file format options.