MINC/VisualTools/register

NAME
MNI-register -  interactive volume display and point tagging program

SYNOPSIS
register [-version]] [-help] [-rgb]] [-cmap]] [-single] [-double] [-global variable value]] [volume1filename] [volume2filename] [tags.tag]

DESCRIPTION
Register is  an interactive graphics application. It can display one or two volumes (typically MR or PET), and the merged image of the two. Some, but not all, versions will allow switching between single and double buffer mode and between RGB  and  colour  map  mode, so the options -rgb, -cmap, -single, -double are useful for setting the initial state of the program. There are three viewports for each volume, showing tranverse, sagittal, coronal slices. The user can  move  throughout  the  volumes,  and create tag points within the volumes. If enough tag points for  two volumes are picked, then a transformation is computed for registering the two volumes. This transform is  used  in displaying  the  merged  image and in allowing the user to start a process which resamples one of  the  volumes  into the same space as the other. A vector volume will normally be converted to an RGB volume, on input. I don't know what that means in terms  of register's display. Alternatively, the vector can be converted to a scalar whose value is the mean of the  vector components, by  setting  the global variable Convertvectorsto_rgb to FALSE.

USER INTERFACE
The user interface is a mouse-based interface composed of buttons,  sliders, and text entry. Buttons can be pressed with the left mouse button. Text entries can be  changed by pressing  the  left  mouse button on them, then typing text. Typing return signals the text entry is done. Typing escape ends text editting without modifying the text. The delete, cursor left, and cursor  right  keys  may  be used. Ctrl-a and ctrl-e move the cursor to the beginning and end of text, respectively. Ctrl-u deletes all text in the text entry.

MAIN MENU
Quit: Quits the program, after confirmation.

Resample and Load: Resamples the second volume to place it in the same space as the first, according to the transformation defined by the tag points. Resample Filename: Text entry to set the name of the file to create for the resampling.

Synced / Not Synced: Toggle switch to control whether the cursor position  in  all volumes is enforced to always be the same.

Flat / Interpolated: Not implemented yet. Eventually will control the interpolation method for display. Colour Map / RGB: Toggles between colour map mode (faster updates) and RGB mode (truer colours).

Double / Single: Toggles between double and single buffer.

Load Tags: Loads a set of tag points into the program.

Tags Filename:  Text  entry to set name of filename to be used by load and save tags. A default extension \".tag\" is provided automatically.

Save Tags: Saves all active tag points to a file. If one volume is loaded, then a set of single tags is saved. If two volumes  are  loaded, then a set of pairs of tags are saved.

Save Transform: Saves the transform defined  by  the  tag points, if it exists.

Transform Filename: Text entry to set name of filename to be used by save transform. A default extension \".xfm\" is provided automatically.

Record Tag:  Overwrites  the  current tag point positions with the current positions within the  volumes. If the current tag point is the end of the tags, then it creates a new tag point.

Delete Tag: Deletes the current tag point.

Delete All Tags: Pops up a confirmation box allowing  you to delete all the tags.

Transform Type: Pops up a dialog to select 6 parameter, 7 parameter, 12 parameter, or thin-plate spline  non-linear fitting.

Tags In/Visible:  Toggles  the display of tag point positions on the slices.

Cursor In/Visible: Toggles the display of cursor crosshair on the slices.

Interp: Flat/Smooth: Toggles the display of slices between flat and smooth shading. Smooth shading takes much longer to update  (a  few  seconds), but produces higher quality images, especially noticeable when the images are  zoomed up.

RMS: Displays the average RMS error of the tag points, if a transform exists.

VOLUME MENUS
Voxel and World Position Readouts Displays the position of the volume  cursor  in  voxel and world coordinates. The positions can be changed numerically by clicking  on  the number and typing in the desired position.

Load Volume: Loads the specified volume.

Volume Filename: Specifies the volume filename.

Reset View: Resets the scale and translation of the slices to fit in the viewports.

Filter Pops up a dialog window that  selects  the  filter type for each of the 3 views of the volume. The filtering applies across slices, but not within slice. The filter types are:  nearest  neighbour, linear interpolation, box filter, triangle filter, and gaussian filter.

Under Colour: Sets the colour displayed for voxels  whose values are less than the range.

Over Colour:  Sets  the colour displayed for voxels whose values are greater than the range.

Colour Bar Slider: Sets the colour range. The left mouse can be used to drag the upper or lower limit. The middle mouse is used to move both at the same time.

Colour Coding Type: Sets the colour coding method to  one of gray scale, hot metal, spectral, red, green, or blue.

MERGED MENU
Voxel and  World Position Readouts: Displays the position of the volume cursor in voxel and world coordinates. The positions can  be  changed numerically by clicking on the number and typing in the desired position.

Reset View: Resets the scale and translation of the slices to fit in the viewports.

Merge Method  Buttons:  Sets  the  merge method to one of blend, weighted, one on two, or two on one. Blend allows blending between  the two volumes. Weighted allows arbitrary weights for the two volumes. One on two places volume one  on  top of volume two, with volume two showing through if volume one is out of range. Two on one is the opposite.

Opacity Sliders Sets the weights of the two volumes. Only used if the merge method is blend or weighted.

TAGS MENU
Position: Displays and allows setting of tag positions.

Name: Sets the name of a tag.

On / Ignore: Sets the activity of a tag, whether it  contributes to the transformation or not.

Dst: Displays  the distance of the tag point in the first volume from the position of the transformed

MOUSE AND KEYBOARD
In the slice viewports, the following actions are valid:

Left Mouse: Sets the volume cursor position.

Middle Mouse: Moves slice perpendicular  according  to  y position of mouse.

Right Mouse:  Adds  a new tag point at the current volume cursor positions.

Shift/Ctrl/Alt Left Mouse: Translates the slice display

Shift/Ctrl/Alt Middle  Mouse:  Zooms  the  slice  display according to the y position of the mouse.

VOLUME CACHING
Register has  the  ability  to handle volumes larger than virtual memory by caching parts of the volume in  memory. The current  default for deciding when to cache is volume is 80 Megabytes. See the  documentation  of  the  source libraries for MNI-register for more information.

Note that volume caching can have a radical effect on performance. In some cases you may get much better results by disabling caching, especially when working with volumes on NFS-mounted filesystems.

To disable caching, set VOLUME_CACHE_THRESHOLD environment variable to -1. I.E in bash

FILES
/usr/local/lib/register.globals

/usr/local/lib/register_UI.globals

AUTHOR
DavidMacDonald