Menus

File

• New
• Open
• Scan
• Open Warped Scan
• * Contours
• * File is a raw 3D block of unsigned characters where each bit plane is a contour.
• * File name is “<result path>/otl/<Segmenter Prefix>_contour.buchar” (and there is an accompanying “<...>.hdr” file)
• * Outlines
• * Outline Files - files containing lists of points with associated labels
  • This Slice
  • All Slices
• * 3D Mask File - image volumes where each voxel value indicates what is there (more info)
  • This Slice
  • All Slices
• * Button: Cancel
• * 3D mask File Name - click to set the file that will be used when the above buttons are pressed)
• Warped Outline
• Surface
• Mask
• Image positions & Views
• Current Program state
• Save
• Scan
• * Contours
• File is a raw 3D block of unsigned characters where each bit plane is a contour.
• File name is “<result path>/otl/<Segmenter Prefix>_contour.buchar” (and there is an accompanying “<...>.hdr” file)
• * Outlines
• * Button: All - saves all slices using the current segmenter prefix
• * Button: Slice - just current slice
• * Button: Cancel
• Image positions & Views
• Current Program state
• Save As
• * Save main Image as *.img files
• 256x256x16bit (no header file)
• Used after positional normalization to save images as new scan
• * Save main image as .ppm file.
• Saves what is showing in main image (without projection lines or landmarks).
• * Save Contour As...
• Allows contour file to be saved in an arbitrary location with an arbitrary name
• * Save Outline As...
• * Button: individal files - Allows new Segmenter prefix to be chosen (for this save only, outline files are called “<result path>/otl/<new Segmenter Prefix><slice#>.otl”).
• * Button: 3D mask (saves all outlines as a singls 3D .buchar mask with .hdr and _map.xml files)
• * Button: Cancel
• Image positions & Views
• Current Program state
• * Quit

Edit

• Undo
• * Cut
• Copy
• Paste
• Erase ALL contours “Super” shift-X
• remove all outlines“Super” shift-W:
• * Cropping
• * Choose Scan
• For multiple scans, selects the one to crop or uncrop.
• * Crop Button
• Uses landmarks MIN_CROP and MAX_CROP to determine what region of the scan to load into memory. This makes the display more efficient in time and screen space.
• * Uncrop Button
• Causes nvm to ignore MIN_CROP and MAX_CROP and to load the entire scan into memory.
• * Positional Normalization
• Uses landmarks, AC_POINT, PC_POINT, and MID_SAGITTAL_POINT to set the view angles such that the main image views a coronal plane with the slice axis along the AC-PC line and with the mid-sagittal point directly above that line. Also, the scan and image centers (about which the rotations take place) are set to the point on the AC-PC line closest to the mid-sagittal point.
• * Print AC,PC,MS Point coordinates
• Calculate and Save Volumes...
• * Output results to spreadsheet
• Output results to database
• Email bug report /comments (with program state)
• * Preferences
• * Buttons
• * Cancel
• * Apply
• * Ok
• * Menus
• * File
• * Help
• General Tabs
• * General
• * Views
• * Outlines
• Contours
• * Windows
• * SegMentor
• * AutoContour
• Keyboard Commands
• Tools Tabs
• Includes a short description of the tool and how to use it.
• * Arrow
• * Contour
• Draw
• Nudge
• Eraser
• Box
• * Landmark
• * Label
• Histogram
• Future

Windows

• * Tile Window
• * AutoContour Window

Help

• About
• * Shows version information & credits
• Help
• * Launches browser