
MrAlign, a new version of mrLoadVol
-----------------------------------
ABP,SPG 7.25.97

NEW BEHAVIOR

 MrAlign allows for a much more accurate match between the
 inplane anatomy and the interpolated volume anatomy by permitting
 rotation in 3 dimensions. It is also cleansed of a lot of obsolete
 baggage and a lot of unsightly bugs in mrLoadVol.

Inplane Grid
------------

 The inplane grid imposed upon the sagittal interpolated image is now
 colored blue. When an inplane is selected, the line turns red. Rotation
 controls in 'Align' menu have been moved to Rotation Control Window

Rotation Control Window
-----------------------

  Window contains buttons for rotating both the sagittal and oblique
  displays in 3 dimensions. Note that the oblique always remains
  orthogonal to the sagittal image, intersecting it through the red
  inplane grid line.

   Joystick

   The joystick-like configuration of buttons on left side of the panel
  rotates the sagittal image (and the oblique if an inplane has been
  selected already) about a pivot centered in the middle of the image.
  'Up' and 'Down' rotate about the axial axis (horizontal axis of
  sagittal image) . Left and Right about the coronal axis. the '0,0'
  button in the center of the 'joystick' returns both interpolated images
  to null rotation. Slider up and to the left of the joystick changes the
  degree of rotation taken with each button press. Leftwards is finer,
  rightwards is coarser.

   Save/Reload Align Params

  mrLoadVol saved its parameters in a file called VolParams. mrAlign reads
  VolParams and saves its own parameter file called AlignParams. The
  'Save' button is the only control which allows the user to save the
  current state of AlignParams, such as the current rotation in 3
  dimensions, the inplane grid clip, the current interpolated inplane,
  etc. 'Reload' restores all the parameters to their most recent saved
  state.

   Inplane grid/Sagittal axis rotation control.

  The buttons to the right side of the panel rotate the interpolated
  images about the sagittal axis running through the middle of the inplane
  grid. The buttons 'Gross' and 'Fine' control the degree of rotation with
  each button press. These controls replace Allen's menu items under the
  Sagittal Window's 'Align' menu. 

Saving: VolParams to AlignParams
--------------------------------

  mrAlign saves its parameters in a file called AlignParams. When you
  start using mrAlign, it will attempt to read a VolParams and copy it to
  AlignParams, so you risk nothing by using mrAlign. 

New Error Message
-----------------

  'Out of range oblique points. Re-Clip Inplanes' This message typically
  means that the bounds for the inplane being selected go out of range of
  the interpolated volume anatomy. This may happen if the inplane grid is
  translated or rotated too far, so that a portion goes out of range.
  Simply reclip the grid until the warnings go away or reconsider your
  rotation.


PRUNED CODE:

list of functions we cleaned out because we thought them obsolete. 
	
mrSaveSagVol
mrSaveOblVol
mrLoadSagVol
mrLoadOblVol
mrExtractOblOld






