08 March 2002:
  * added plug_crender.c

21 May 2002:
  * added rickr directory containing r_idisp.[ch], r_misc.[ch],
      r_new_resam_dset.[ch] and Makefile
  * added new program 3dresample (rickr/3dresample.c)
  * modified Makefile.INCLUDE to build rickr directory

06 June 2002:
  * added @SUMA_Make_Spec_FS

20 June 2002:
  * added @make_stim_file

21 June 2002:
  * modified afni_plugin.c, NLfit_model.c and thd_get1D.c to
      validate directories
  * added rickr/AFNI.changes.rickr

01 July 2002:
  * added rai orientation to plug_crender.c
  * added plug_crender.so target to Makefile.INCLUDE for use of librickr.a

02 July 2002:
  * modified 3dresample
      - fully align dataset to the master (not just dxyz and orient)
      - removed '-zeropad' option (no longer useful with new alignment)
  * modified r_new_resma_dset.[ch]
      - r_new_resam_dset() now takes an additional mset argument, allowing
        a master alignment dataset (overriding dxyz and orient inputs)
  * modified plug_crender.c to pass NULL for the new mset argument to
      r_new_resam_dset()
  * modified @SUMA_AlignToExperiment, removing '-zeropad' argument when
      running program 3dresample

15 July 2002:
  * added @SUMA_Make_Spec_SF and @make_stim_file to SCRIPTS in Makefile.INCLUDE

29 July 2002:
  * modified plug_crender.c to allow arbitrary orientation and grid spacing
      of functional overlay (no longer needs to match underlay)
  * modified r_new_resam_dset.c to set view type to that of the master
  * updated VERSION of 3dresample to 1.2 (to note change to r_new_resam_dset)

05 August 2002:
  * modified plug_crender.c (rv 1.5) to align crosshairs with master grid
  * added ENTRY() and RETURN() statements

11 September 2002:
  * added rickr/file_tool.[ch]
  * modified rickr/Makefile and Makefile.INCLUDE to be able to build file_tool
    (note that file_tool will not yet be built automatically)
  * modified r_idisp.c to include r_idisp_vec3f()

20 September 2002:
  * modified thd_opendset.c so that HEAD/BRIK are okay in directory names
    (see 'fname' and 'offset' in THD_open_one_dataset())

26 September 2002:
  * modified plug_crender.c
      - calculate and draw crosshairs directly
      - added debugging interface (access via 'dh' in opacity box)
  * modified cox_render.[ch] - pass rotation matrix pointer to CREN_render()
  * modified testcox.c - pass NULL to CREN_render() for rotation matrix pointer

01 October 2002:
  * modified Makefile.INCLUDE to build file_tool automatically

23 October 2002:
  * modified plug_crender.c so that Incremental rotation is the default

29 October 2002:
  * modified plug_second_dataset.c and plug_nth_dataset.c to update dataset
      pointers from idcodes on a RECEIVE_DSETCHANGE notification

22 November 2002:
  * added new program Hfile, including files rickr/Hfile.[ch]
  * modified rickr/Makefile and Makefile.INCLUDE to build Hfile

27 November 2002:
  * Hfile is now Imon
  * many modifications to Imon.[ch] (formerly Hfile.[ch])
      - see rickr/Imon.c : history for version 1.2
  * renamed Hfile.[ch] to Imon.[ch]
  * modified rickr/Makefile to reflect the name change to Imon
  * modified Makefile.INCLUDE to reflect the name change to Imon

13 December 2002:
  * Imon no longer depends on Motif
      - mcw_glob.[ch] are used locally as l_mcw_glob.[ch]
      - Imon.c now depends only on l_mcw_glob.[ch]
      - rickr/Makefile now compiles Imon.c and l_mcw_glob.c
        with -DDONT_USE_MCW_MALLOC

14 January 2003:
  * update 3dresample to clear warp info before writing to disk

15 January 2003:
  * The highly anticipated release of Imon 2.0!!
      - Imon now has optional rtfeedme functionality.
      - add files rickr/realtime.[ch]
      - modified rickr/Imon.[ch]
      - modified rickr/Makefile
          o to build .o files with -DDONT_USE_MCW_MALLOC
          o to use $(EXTRA_LIBS) for sockets on solaris machines
      - modified Makefile.INCLUDE
          o Imon now also depends on rickr/realtime.[ch]
          o pass $(EXTRA_LIBS) to the make under rickr

27 January 2003:
  * modified Makefile.solaris28_gcc : defined EXTRA_LIBS_2
      (is EXTRA_LIBS without -lgen and -ldl)
  * modified Makefile.INCLUDE for Imon to use EXTRA_LIBS_2
  * modified rickr/Makefile for Imon to use EXTRA_LIBS_2

28 January 2003:
  * modified Imon.[ch] to add '-nt VOLUMES_PER_RUN' option (revision 2.1)

02 February 2003:
  * modified Imon.[ch] to fail only after 4 I-file read failures (rv 2.2)

10 February 2003:
  * added a new SUMA program, 3dSurfMaskDump
      o added files SUMA/SUMA_3dSurfMaskDump.[ch]
      o modified SUMA_Makefile to make 3dSurfMaskDump
      o modified Makefile.INCLUDE, targets:
	    suma_exec, suma_clean, suma_link, suma_install
  * modified Makefile.solaris2[67]_gcc, defining EXTRA_LIBS_2

11 February 2003:
  * minor updates to SUMA/SUMA_3dSurfMaskDump.c (for -help)
  * 3dSurfMaskDump rv 1.2: do not free structs at the end

13 February 2003:
  * 3dSurfMaskDump rv 1.2: redo rv1.2: free structs conditionally (and init)

14 February 2003:
  * 3dSurfMaskDump rv 1.3: optionally enable more SUMA debugging
  * modified Imon.[ch] (rv 2.3): added '-start_file' option

18 February 2003:
  * modified Imon.[ch] (rv 2.4), realtime.[ch]
      o added DRIVE_AFNI command to open a graph window (-nt points)
      o added '-drive_afni' option, to add to the above command
      o pass Imon command as a dataset NOTE
  * modified rickr/Makefile - added WARN_OPT

20 February 2003:
  * modified rickr/Imon.[ch] rickr/realtime.c (Imon rv 2.5)
      o appropriately deal with missing first slice of first volume
      o separate multiple DRIVE_AFNI commands
      o minor modifications to error messages

28 February 2003:
  * modified rickr/file_tool.[ch]: added '-quiet' option

25 March 2003:
  * modified Imon to version 2.6: Imon.[ch] realtime.[ch]
      o added -GERT_Reco2 option to output script
      o RT: only send good volumes to afni
      o RT: added -rev_byte_order option
      o RT: also open relevant image window
      o RT: mention starting file in NOTE command

01 May 2003:
  * modified mcw_glob.c and rickr/l_mcw_glob.c
	- removed #ifdef around #include <errno.h>
  * modified imseq.c - added #include <errno.h>

06 May 2003:
  * file_tool 1.3 - added interface for GEMS 4.x image files
      o added ge4_header.[ch]     - all of the processing for 4.x images
      o added options for raw data display (disp_int2, disp_int4, disp_real4)
      o modified file_tool.[ch]   - interface to ge4
      o modified rickr/Makefile   - file_tool depends on ge4_header.o
      o modified Makefile.INCLUDE - file_tool depends on ge4_header.o

09 May 2003:
  * modified 3dmaskdump.c
      o added -index option for Mike B
      o combined changes with Bob's

28 May 2003:
  * added SUMA/SUMA_3dSurf2Vol.[ch]

29 May 2003:
  * modified Makefile.INCLUDE and SUMA/SUMA_Makefile to build 3dSurf2Vol
  * 3dSurf2Vol (version 1.0) is now part of the suma build
  * file_tool version 2.0 : added ge4 study header info
      o modified ge4_header.[ch] rickr/file_tool.[ch]

03 June 2003:
  * modified ge4_header.[ch] to be called from mri_read.c
  * modified mri_read.c - added mri_read_ge4 and call from mri_read_file()
  * modified mrilib.h - added declaration for mri_read_ge4()
  * modified Makefile.INCLUDE - added ge4_header.o to MRI_OBJS for mri_read_file
  * modified file_tool (version 2.1) for slight change to ge4_read_header()

06 June 2003:
  * modified SUMA_3dSurfMaskDump.[ch]
      o now 3dSurfMaskDump version 2.0
      o re-wrote program in terms of 3dSurf2Vol, to handle varying map types
      o added 'midpoint' map function

12 June 2003:
  * modifed SUMA_3dSurf2Vol.c - minor changes to help and s2v_fill_mask2()
  * modifed ge4_header.c to remove "static" warnings

17 June 2003:
  * modified SUMA_3dSurfMaskDump.[ch] -> version 2.1
      o added 'ave' map function

19 June 2003:
  * modified SUMA_3dSurfMaskDump.[ch] -> version 2.2
      o added -m2_index INDEX_TYPE for the option of indexing across nodes
      o set the default of -m2_steps to 2
      o replace S2V with SMD in macros
  * modified SUMA_ParseCommands.c
      o In SUMA_FreeMessageListData(), do not free Message or Source, as
        they are added as static or local strings (but never alloc'd).

26 June 2003:
  * modified Imon.[ch], realtime.c to add axis offset functionality
      -> Imon version 2.7

27 June 2003:
  * modified Imon.c, realtime.c to pass BYTEORDER command to realtime plugin
      -> Imon version 2.8
  * modified plug_realtime.c to handle BYTEORDER command

30 June 2003:
  * modified README.realtime to provide details of the BYTEORDER command
  * modified plug_realtime.c to accept BYTEORDER for MRI_complex images

21 July 2003:
  * modified SUMA_3dSurfMaskDump.[ch] -> version 2.3
      - fixed a problem: voxels outside gpar dataset should be skipped (or
	get a special value, like 0)
      - added min/max distance output (at debug level > 0)

22 July 2003:
  * modified plug_crender.c to handle bigmode color bar (version 1.8)
      ** need to add bigmode information to widget storage
  * modified SUMA_3dSurf2Vol.[ch] -> version 1.2
      - see 3dSurfMaskDump: skip nodes outside dataset space

27 July 2003:
  * modified 3dresample.c (v1.4), file_tool.[ch] (v2.2), Imon.c (v2.9),
    realtime.[ch] (v2.9), r_idisp.[ch] (v1.2) - added CHECK_NULL_STR() to
    questionable strings for printing (old glibc doesn't print (nil))
  * modified Imon.h - increase IFM_EPSILON to 0.01 and IFM_MAX_DEBUG to 4

05 August 2003:
  * renamed SUMA_3dSurfMaskDump.[ch] to SUMA_3dVol2Surf.[ch]
  * modified Makefile.INCLUDE and SUMA/SUMA_Makefile_NoDev for 3dVol2Surf
  * modified SUMA_3dVol2Surf (major re-write -> version 3.0)
      - all output functions now go through dump_surf_3dt
      - dump_surf_3dt() is a generalized function to get an MRI_IMARR for one
        or a pair of nodes, by converting to a segment of points
      - added v2s_adjust_endpts() to apply segment endpoint modifications
      - added segment_imarr() to get the segment of points and fill the
        MRI_IMARR list (along with other info)
      - filter functions have been taken to v2s_apply_filter()
      - added min, max and seg_vals map functions (filters)
      - added options of the form -f_pX_XX to adjust segment endpoints
      - added -dnode option for specific node debugging
      - changed -output option to -out_1D
      - added new debug info
      - added checking of surface order (process from inner to outer)
  * modified Imon (-> v2.10): added '-sp SLICE_PATTERN' option

14 August 2003:
  * modified Imon.[ch], realtime.h:
      - added '-quit' option
      - allow both 'I.*' and 'i.*' filenames
      
15 August 2003:
  * modified 3dDeconvolve.c   - only output timing with -jobs option
  * modified Makefile.INCLUDE - fix cygwin compile
      - created PROGRAM_EXE targets for Imon.exe, file_tool.exe, 3dresample.exe

20 August 2003:
  * modified Imon.c (-> v3.0)  - retest errors before reporting them
      - major version change for high numbers, plus new warning output

02 September 2003:
  * modified Imon.c (->v3.1) - added '-gert_outdir OUTPUT_DIR' option

08 September 2003:
  * modified L_CREATE_SPEC write error to name correct directory

11 September 2003:
  * modified 3dfim+.c: read_one_time_series() was still using old 'filename'

17 September 2003:
  * modified SUMA_3dVol2Surf.c: fixed help info for '-cmask option'

21 September 2003:
  * modifited SUMA_3dVol2Surf.c:
      - added max_abs mapping function
      - added '-oob_index' and '-oob_value' options
      - added CHECK_NULL_STR macro

23 September 2003:
  * modifited SUMA_3dVol2Surf.c: added help for -no_header option

01 October 2003:
  * modified SUMA_3dVol2Surf.c: added -oom_value option and help example

02 October 2003:
  * major upgrades to 3dSurf2Vol (-> v2.0)
      - changes accepting surface data, surface coordinates, output data type,
        debug options, multiple sub-brick output, and segment alterations
      - added the following options:
	  '-surf_xyz_1D', '-sdata_1D', '-data_expr', '-datum', '-dnode',
	  '-dvoxel', '-f_index', '-f_p1_fr', '-f_pn_fr', '-f_p1_mm', '-f_pn_mm'

06 October 2003:
  * modified 2dImReg.c: is nsl == 0, use nzz for num_slices

07 October 2003:
  * modified plug_roiedit.[ch]: old/new -> Bold/Bnew for C++ compilation

08 October 2003:
  * modified @SUMA_AlignToExperiment to use tcsh instead of csh (for $#)

20 October 2003:
  * modified SUMA files SUMA_Load_Surface_Object.[ch] SUMA_MiscFunc.[ch] and
    SUMA_Surface_IO.[ch] to make non-error output optional via a debug flag
      - renamed the following functions to XXX_eng (engine functions):
          SUMA_Load_Surface_Object, SUMA_LoadSpec, SUMA_SurfaceMetrics,
          SUMA_Make_Edge_List, SUMA_FreeSurfer_Read
      - wrote functions with original names to call engines with debug
        flags set
  * modified SUMA_3dVol2Surf.c to call the new SUMA_LoadSpec_eng()   (-> v3.5)
  * modified SUMA_3dSurf2Vol.c to call the new SUMA_LoadSpec_eng()   (-> v2.1)
  * modified rickr/r_idisp.c to handle new ALLOW_DATASET_VLIST macro (-> v1.3)

21 October 2003:
  * modified SUMA_3dVol2Surf.c to complete the -f_keep_surf_order option
    (-> v3.6)

30 October 2003:
  * modifited 3dbucket.c to search for trailing view type extension from end
    (under -glueto option processing)
  * modified plug_realtime.c to compute function on registered data

05 November 2003:
  * modified SUMA_3dVol2Surf.c to include ENTRY() stuff (3dVol2Surf -> v3.7)

07 November 2003:
  * checked in an initial version of SurfMeasures (v0.2)
      - this is not a release version (this checkin is for backup)
      - supported functions are coord_A, coord_B, n_area_A, n_area_B,
        nodes, node_vol and thick

14 November 2003:
  * updates to SurfMeasures (v0.3 - not yet released)

19 November 2003:
  * more updates to SurfMeasures (v0.5)

01 December 2003:
  * finally!!  SurfMeasures is ready for release (v1.0)
      - checked in v1.0 of SUMA/SUMA_SurfMeasures.[ch]
  * modified Makefile.INCLUDE for SurfMeasures
  * modified SUMA/SUMA_Makefile_NoDev for SurfMeasures

03 December 2003
  * modified SUMA/SUMA_SurfMeasures.[ch]  (v1.2)
      - added '-cmask' and '-nodes_1D' options

16 December 2003
  * modified SUMA_Load_Surface_Object.[ch]
      - added functions: SUMA_spec_select_surfs(), SUMA_swap_spec_entries(),
        SUMA_unique_name_ind(), SUMA_coord_file(), swap_strings()
      - made change to restrict spec struct (and therefore surface loading)
        to surfaces named in a list
  * modified SUMA_SurfMeasures.[ch] (-> SurfMeasures v1.3)
      - added '-surf_A' and '-surf_B' to specify surfaces from the spec file
        (goes through new function SUMA_spec_select_surfs())
      - fixed loss of default node indices (from -nodes_1D change)
      - added '-hist' option
      - display angle averages only if at least 1 total is computed
  * modified SUMA_3dVol2Surf.[ch] (-> 3dVol2Surf v3.8)
      - added '-surf_A' and '-surf_B' to specify surfaces from the spec file
      - depreciated option '-kso'
      - added '-hist' option
  
18 December 2003
  * modified SUMA_3dSurf2Vol[ch] (-> 3dSurf2Vol v2.2)
      - added '-surf_A' and '-surf_B' to specify surfaces from the spec file
      - added '-hist' option
  * modified SUMA_3dSurf2Vol[ch] (-> 3dSurf2Vol v3.0)
      - removed requirement of 2 surfaces for most functions
        (this was not supposed to be so easy)

22 December 2003
  * modified afni_graph.[ch] to add Mean and Sigma to bottom of graph window

07 January 2004
  * modified 3dresample.c
      - added suggestion of 3dfractionize to -help output
      - added -hist option

13 January 2004
  * modified Imon.[ch] realtime.[ch]
      - added '-zorder ORDER' option for slice patterns in real-time mode
        (the default has been changed from 'seq' to 'alt')
      - add '-hist' option

22 January 2004
  * modified SUMA_3dVol2Surf.[ch]  (-> 3dVol2Surf v3.9)
      - added use of normals to compute segments, instead of second surface
        (see options '-use_norms', '-norm_len', '-keep_norm_dir')
      - reversed order of '-hist' output
  * modified SUMA_SurfMeasures.[ch] (-> SurfMeasures v1.4)
      - fixed node coord output error when '-nodes_1D' gets used
      - added '-sv' option to examples (recommended)
      - reversed order of '-hist' output

23 January 2004
  * modified SUMA_3dVol2Surf.c, SUMA_3dSurf2Vol.c and SUMA_SurfMeasures.c
             ( -> v4.0            -> v3.1              -> v 1.5 )
      - SUMA_isINHmappable() is depricated, check with AnatCorrect field

29 January 2004
  * modified plug_realtime.c :
      - allow 100 chars in root_prefix via PREFIX (from 31)
      - x-axis of 3-D motion graphs changed from time to reps
      - plot_ts_... functions now use reg_rep for x-axis values
      - reg_graph_xr is no longer scaled by TR
      - added (float *)reg_rep, for graphing with x == rep num
      - added RT_set_grapher_pinnums(), to call more than once
      - added GRAPH_XRANGE and GRAPH_YRANGE command strings for control over
        the scales of the motion graph
      - if GRAPH_XRANGE and GRAPH_YRANGE commands are both passed, do not
        display the final (scaled) motion graph
  * modified README.realtime with details on GRAPH_XRANGE and GRAPH_YRANGE

10 February 2004:
  * modified  SUMA_3dSurf2Vol.c (-> v3.2) to add debug output for AnatCorrect
  * modified  SUMA_3dVol2Surf.c (-> v4.1) to add debug output for AnatCorrect

11 February 2004:
  * modified  SUMA_SurfMeasures.c (-> v1.6) to add debug output for AnatCorrect

13 February 2004:
  * modified README.realtime to include the GRAPH_EXPR command
  * modified plug_realtime.c:
      - added RT_MAX_PREFIX for incoming PREFIX command
      - if GRAPH_XRANGE or GRAPH_YRANGE is given, disable respective 'pushing'
      - added GRAPH_EXPR command, as explained in README.realtime
      - added parser functionality to convert 6 graphs to 1 via the expression
  * modified Imon.[ch], realtime.[ch] -> (Imon v3.3)
      - added '-rt_cmd' option for passing commands to the realtime plugin
      - the '-drive_cmd' option can now be used multiple times
      - the realtime zorder is defaulting to seq again (affects physical order)
      - passed lists of drive and RT commands to realtime plugin

18 February 2004:
  * modified SUMA_3dVol2Surf.[ch] (->v4.2) 
      - add functionality for mapping functions that require sorting
      - added mapping functions 'median' and 'mode'

19 February 2004:
  * modified SUMA_3dVol2Surf.[ch] (->v4.3) to track 1dindex sources 

20 February 2004:
  * modified plug_maxima.c
      - added ENTRY/RETURN calls
      - error: do not process last plane in find_local_maxima()

23 February 2004:
  * modified mri_dup.c to allow NN interpolation if AFNI_IMAGE_ZOOM_NN is Y
  * modified afni_pplug_env.c to add control for AFNI_IMAGE_ZOOM_NN
  * modified README.environment to add a description of AFNI_IMAGE_ZOOM_NN
  * modified SUMA_SurfMeasures.[ch] to add functions:
      'n_avearea_A', 'n_avearea_B', 'n_ntri'

