


REGISTER(1)                                           REGISTER(1)


NNAAMMEE
       MNI-register  -  interactive volume display and point tag-
       ging program

SSYYNNOOPPSSIISS
       rreeggiisstteerr  [-rgb]   [-cmap]   [-single]   [-double]   [vol-
       ume1_filename] [volume2_filename]

DDEESSCCRRIIPPTTIIOONN
       _R_e_g_i_s_t_e_r  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.

UUSSEERR IINNTTEERRFFAACCEE
       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.  Typ-
       ing 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.


MMAAIINN MMEENNUU
       _Q_u_i_t_: Quits the program, after confirmation.

       _R_e_s_a_m_p_l_e _a_n_d _L_o_a_d_: Resamples the second volume to place it
       in the same space as the first, according to the transfor-
       mation defined by the tag points.

       _R_e_s_a_m_p_l_e _F_i_l_e_n_a_m_e_: Text entry to set the name of the  file
       to create for the resampling.

       _S_y_n_c_e_d  _/ _N_o_t _S_y_n_c_e_d_: Toggle switch to control whether the
       cursor position in all volumes is enforced  to  always  be
       the same.

       _F_l_a_t _/ _I_n_t_e_r_p_o_l_a_t_e_d_: Not implemented yet.  Eventually will
       control the interpolation method for display.



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REGISTER(1)                                           REGISTER(1)


       _C_o_l_o_u_r _M_a_p _/ _R_G_B_: Toggles between colour map mode  (faster
       updates) and RGB mode (truer colours).

       _D_o_u_b_l_e _/ _S_i_n_g_l_e_: Toggles between double and single buffer.

       _L_o_a_d _T_a_g_s_: Loads a set of tag points into the program.

       _T_a_g_s _F_i_l_e_n_a_m_e_: Text entry to set name of  filename  to  be
       used by load and save tags.  A default extension ".tag" is
       provided automatically.

       _S_a_v_e _T_a_g_s_: 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.

       _S_a_v_e  _T_r_a_n_s_f_o_r_m_:  Saves  the  transform defined by the tag
       points, if it exists.

       _T_r_a_n_s_f_o_r_m _F_i_l_e_n_a_m_e_: Text entry to set name of filename  to
       be  used by save transform.  A default extension ".xfm" is
       provided automatically.

       _R_e_c_o_r_d _T_a_g_: 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.

       _D_e_l_e_t_e _T_a_g_: Deletes the current tag point.

       _D_e_l_e_t_e  _A_l_l  _T_a_g_s_: Pops up a confirmation box allowing you
       to delete all the tags.

       _T_r_a_n_s_f_o_r_m _T_y_p_e_: Pops up a dialog to select 6 parameter,  7
       parameter,  12  parameter, or thin-plate spline non-linear
       fitting.

       _T_a_g_s _I_n_/_V_i_s_i_b_l_e_: Toggles the display of  tag  point  posi-
       tions on the slices.

       _C_u_r_s_o_r _I_n_/_V_i_s_i_b_l_e_: Toggles the display of cursor crosshair
       on the slices.

       _I_n_t_e_r_p_: _F_l_a_t_/_S_m_o_o_t_h_: 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.

       _R_M_S_: Displays the average RMS error of the tag points,  if
       a transform exists.






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REGISTER(1)                                           REGISTER(1)


VVOOLLUUMMEE MMEENNUUSS
       _V_o_x_e_l _a_n_d _W_o_r_l_d _P_o_s_i_t_i_o_n _R_e_a_d_o_u_t_s 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.

       _L_o_a_d _V_o_l_u_m_e_: Loads the specified volume.

       _V_o_l_u_m_e _F_i_l_e_n_a_m_e_: Specifies the volume filename.

       _R_e_s_e_t _V_i_e_w_: Resets the scale and translation of the slices
       to fit in the viewports.

       _F_i_l_t_e_r  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.

       _U_n_d_e_r  _C_o_l_o_u_r_:  Sets the colour displayed for voxels whose
       values are less than the range.

       _O_v_e_r _C_o_l_o_u_r_: Sets the colour displayed  for  voxels  whose
       values are greater than the range.

       _C_o_l_o_u_r  _B_a_r _S_l_i_d_e_r_: 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.

       _C_o_l_o_u_r  _C_o_d_i_n_g  _T_y_p_e_: Sets the colour coding method to one
       of gray scale, hot metal, spectral, red, green, or blue.


MMEERRGGEEDD MMEENNUU
       _V_o_x_e_l _a_n_d _W_o_r_l_d _P_o_s_i_t_i_o_n _R_e_a_d_o_u_t_s_: 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.

       _R_e_s_e_t _V_i_e_w_: Resets the scale and translation of the slices
       to fit in the viewports.

       _M_e_r_g_e _M_e_t_h_o_d _B_u_t_t_o_n_s_: 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  arbi-
       trary weights for the two volumes.  One on two places vol-
       ume one on top of volume  two,  with  volume  two  showing
       through  if volume one is out of range.  Two on one is the
       opposite.

       _O_p_a_c_i_t_y _S_l_i_d_e_r_s Sets the weights of the two volumes.  Only
       used if the merge method is blend or weighted.





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REGISTER(1)                                           REGISTER(1)


TTAAGGSS MMEENNUU
       _P_o_s_i_t_i_o_n_: Displays and allows setting of tag positions.

       _N_a_m_e_: Sets the name of a tag.

       _O_n  _/  _I_g_n_o_r_e_: Sets the activity of a tag, whether it con-
       tributes to the transformation or not.

       _D_s_t_: Displays the distance of the tag point in  the  first
       volume from the position of the  transformed


MMOOUUSSEE AANNDD KKEEYYBBOOAARRDD
       In the slice viewports, the following actions are valid:

       _L_e_f_t _M_o_u_s_e_: Sets the volume cursor position.

       _M_i_d_d_l_e  _M_o_u_s_e_:  Moves  slice  perpendicular according to y
       position of mouse.

       _R_i_g_h_t _M_o_u_s_e_: Adds a new tag point at  the  current  volume
       cursor positions.

       _S_h_i_f_t_/_C_t_r_l_/_A_l_t _L_e_f_t _M_o_u_s_e_: Translates the slice display

       _S_h_i_f_t_/_C_t_r_l_/_A_l_t  _M_i_d_d_l_e  _M_o_u_s_e_:  Zooms  the  slice  display
       according to the y position of the mouse.


VVOOLLUUMMEE CCAACCHHIINNGG
       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.


AAUUTTHHOORR
       David MacDonald

BBUUGGSS
       Sometimes turning the tags visibilities off does not  turn
       them off.

       On  Indigo  systems,  the  colour maps can get screwed up,
       especially when sliding the colour bar  limits.   In  this
       case,  iconize  then  deiconize  the window to restore the
       colour maps.  To avoid  this  altogether,  switch  to  RGB
       mode.   Current  releases have minimized the occurrence of
       this bug.

       Sometimes you have to hit the over-colour or  under-colour
       button twice for it to notice.




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REGISTER(1)                                           REGISTER(1)


       In  smooth  interpolation  mode,  filtering  has  not been
       implemented.

BBUUGG RREEPPOORRTTSS TTOO
       David MacDonald           david@bic.mni.mcgill.ca

CCOOPPYYRRIIGGHHTTSS
       ((CC)) Copyright 1993 by David MacDonald

















































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