Features: Other Tools

AutoContours

• Like previous "Nauty guesses":
• Assign intensities that can be automatically drawn in a given color, interpolated between values at specific slices, initialized by AutoSeg. Check ends, middle, and in between until they can be interpolated to be correct.
• File Menu
• * New: Clear current AutoContours
• * Open: Load AutoContour file
• * Close: Clear current AutoContours
• * Save: Write AutoContour file
• * Save As: Write AutoContour file with new name
• * Revert to Nautilos Variable File: clear current AutoContours and initialize them from the Nautilos Variable file
• * Hide: hide AutoContour Window
• * Click on AutoContour 's label to set current contour to AutoContour's intensity
• * Choose a contour color to assign to an AutoContour so it will be drawn when changing slices
• * Enter new AutoContour intensity (which is interpolated to the next set AutoContour
• Options
• * Draw AutoContours when changing slices
• * Interpolate neighbors when setting intensity
• * Set intensity of currently selected AutoContour to the current contour intensity
• * Revert AutoContour to initial intensity
• * Add New AutoContour
• * Help (bring up help in browser)
• * Hide window
• Show small graph of AutoContour values indicating which are set and which are interpolated.

SegMentor

• Purpose:
• To explicitly define and imbed neuroanatomical methods into the measurement software. This is a macro interpreter that can do things such as: event logging, make macro from event log, indicate a sequence of labels to assign, provide text descriptions of each border, give instructions on how to extract each border, bring up example pictures of segmented structures and border locations in a browser, make Bug reporting from log, run external (e.g. UNIX) commands, and switch control to other named macros.
• Menus
• * File - open/close SegMentor Scripts (stored as XML)
• * New
• * Open
• * Close
• * Save
• * Save As
• * Hide
• Edit
• Undo
• * Actions
• * Record Events

Keeps a log of events in the main program that can be saved and played back.
• * Record Text

Text is displayed to tell what is happening and remind user what to do next.
• * Play

Run the currently loaded SegMentor Script
• * View

Show each step of the current SegMentor Script
• * Help
• * Help Index
• * About SegMentor
• Buttons & Keys
• * Help
• Launches browser to display general help for loaded script.
• * Previous
• Shows previous statement in SegMentor Script
• * Next
• Shows next statement in SegMentor Script
• * To Do List
• Opens SegMentor Task List window.
• * “Skip Backward” arrow
• Skip commands going backwards, find and show nearest Text display.
• * “Re-Do” (circular) arrow
• Re-execute current step in SegMentor script
• * “Skip Forward” arrow
• Skip commands going forwards, find and show nearest Text display.
• * Misc1, Misc2
• Used by specific commands in scripts. Button text and action are determined by script.
• * “Segmentation Man” Picture
• Launches browser providing help
• “a” or Enter key in image window executes next step in SegMentor script.
• * Status Display
• Indicates what SegMentor is currently doing (shows SegMentor "State")
• * Text Display
• Displays user-provided text (with a scroll bar if necessary)
• * Macro Language
• Simple C-like interpreter
• Can control everything the user can control
• * SegMentor Task List window
• * “Sub-task” buttons are grouped as “tasks” and have individual Help buttons
• * Creates buttons for each “sub-task” (group of SegMentor commands in a separate script)
• * Checkbox for when script is done (either clicked by user or set when going from one task to another)
• * The first sub-tasks are “prerequisites” that must be checked before the rest of the non-prerequisite sub-task buttons are activated
• * “Hide” button
• “Smart” Scripts?
• SegMentor should know approximately which rules might need to be applied for each slice of the scan. (use probabilistic atlas for this?)

Probabilistic atlas (plugin?)