AFNI file: AFNI.changes.rickr
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:
* modified SUMA_3dSurf2Vol.c - minor changes to help and s2v_fill_mask2()
* modified 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:
* modified SUMA_3dVol2Surf.c:
- added max_abs mapping function
- added '-oob_index' and '-oob_value' options
- added CHECK_NULL_STR macro
23 September 2003:
* modified 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: if 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:
* modified 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:
* Added SUMA_SurfMeasures.[ch] -> SurfMeasures (v0.2)
- this is not a release version (this check-in 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 deprecated, 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'
01 March 2004:
* fixed mbig.c (was using AFMALL() without #include), left malloc() for speed
04 March 2004:
* modified 3dresample.c to check RESAM_shortstr, reversed history
08 March 2004:
* modified 3dFWHM.c to output NO_VALUE when results cannot be computed
15 March 2004:
* modified 3dfim+.c: init sum to 0.0 in set_fim_thr_level()
17 March 2004:
* modified file_tool.[ch] (-> v3.0), adding binary data editing
(this was the original goal of the program, yet it took 18 months...)
- added ability to modify 1, 2 or 4-byte signed or unsigned ints
- added ability to modify 4 or 8-byte reals (floats or doubles)
- added '-ge_off' option to display file offsets for certain GE fields
- added '-hist' option to display module history
24 March 2004:
* modified file_tool.c (-> v3.2), only check max length for mods
30 March 2004:
* made history notes of ziad's added argument to SUMA_LoadSpec_eng()
- 3dSurf2Vol (v3.3), 3dVol2Surf (v4.4), SurfMeasures (v1.8)
31 March 2004:
* added rickr/serial_helper.c (-> v1.0)
- this tcp server passes registration correction params to a serial port
* modified plug_realtime.c
- added the ability to pass registration correction parameters over
a tcp socket (see 'serial_helper -help')
* modified afni_pplug_env.c, adding AFNI_REALTIME_MP_HOST_PORT
* modified README.environment, describing AFNI_REALTIME_MP_HOST_PORT
* modified Makefile.INCLUDE, for building serial_helper
* modified rickr/Makefile, for building serial_helper
01 April 2004:
* modified rickr/serial_helper.c (-> v1.2)
- adding a little more help
- checking for bad options
02 April 2004:
* modified rickr/serial_helper.c [request of tross] (-> v1.3)
- change default min to -12.7, and use -128 for serial start signal
* modified plug_realtime.so [request of tross]
- move RT_mp_comm_close() out of check for resize plot
07 April 2004:
* modified SUMA_3dVol2Surf.c (-> v4.5) to fix default direction of normals
* modified serial_helper.c (-> v1.4) to #include sys/file.h for Solaris
* modified Makefile.INCLUDE to pass EXTRA_LIBS_2 for serial_helper build
* modified rickr/Makefile to apply EXTRA_LIBS_2 for Solaris build
13 May 2004:
* added -NN help info to 3drotate.c
17 May 2004:
* modified edt_dsetitems.c: THD_deplus_prefix() to remove only the basic
three extensions: +orig, +acpc, +tlrc (blame Shruti)
18 May 2004:
* modified SUMA_3dVol2Surf.[ch] (-> v5.0)
- allow niml output via '-out_niml'
- accept '-first_node' and '-last_node' options for restricted output
19 May 2004:
* modified coxplot/plot_ts.c:init_colors() to start with color 0 (not 1)
(allows users to modify ...COLOR_01, too, matching README.environment)
20 May 2004:
* modified SUMA_3dVol2Surf.c (-> v5.1)
- Ziad reminded me to add help for options '-first_node' and '-last_node'
07 June 2004:
* modified @RenamePanga - subtract 1 from init of Nwhatapain
21 June 2004:
* modified SUMA_3dSurf2Vol.[ch] (-> v3.4): fixed -surf_xyz_1D option
07 July 2004:
* modified 3dROIstats - added -minmax, -nzminmax options
20 July 2004:
* modified 3dANOVA3.c to fix stack space problem (see N_INDEX)
22 July 2004:
* modified SUMA_3dSurf2Vol.c (-> v3.5) fixed bug in sdata_1D file test
26 July 2004:
* modified thd_mastery.c
- changed THD_setup_mastery() to return int
- added THD_copy_dset_subs(), to copy a list of sub-bricks
* modified 3ddata.h: added declaration for THD_copy_dset_subs()
* modified r_new_resam_dset.[ch], taking new sublist parameter
* modified 3dresample.c (-> v1.7), passing NULL for sublist
* modified plug_crender.c (-> v1.9a), temporary update, passing sublist NULL
27 July 2004:
* modified plug_crender.c (-> v1.9) to resample only appropriate sub-bricks
28 July 2004:
* modified SUMA_3dSurf2Vol.c (-> v3.6), fixed bug where a previous change
caused the default f_steps to revert from 2 to 1 (discovered by Kuba)
02 August 2004:
* modified SUMA_SurfMeasures.c (-> v1.9), do not require anat correct
* modified SUMA_glxdino.c, cast each 3rd gluTessCallback arg as _GLUfuncptr
(some 64-bit machines have complained)
03 August 2004:
* modified f2cdir/rawio.h, hiding read/write declarations for 64-bit machines
* added Makefile.solaris9_suncc_64
* added Makefile.linux_gcc33_64 (for Fedora Core 2, x86-64)
* modified SUMA_glxdino.c, SUMA_pixmap2eps.c to cast gluTessCallback()'s
3rd argument only in the case of the LINUX2 define
11 August 2004:
* SUMA_SurfMeasures.c (-> v1.10) to warn users about ~10% inaccuracy in volume
26 August 2004:
* modified FD2.c: added -swap_yes and -swap_no options
27 August 2004:
* modified FD2.c: replace -swap_yes and -swap_no with a plain -swap
(this alters the original program!)
01 September 2004:
* modified 3dVol2Surf (-> v6.0)
- created vol2surf() library files vol2surf.[ch] from core functions
- this represents a significant re-write of many existing functions,
modifying locations of action, structure names/contents, etc.
- add library to libmri (as this will end up in afni proper)
- separate all vol2surf.[ch] functions from SUMA_3dVol2surf.[ch]
- keep allocation/free action of results struct within library
- now using SUMA_surface struct for surface info (replace node_list)
- added main vol2surf(), afni_vol2surf(), free_v2s_results(),
and disp...() functions as vol2surf library interface
- added options to control column output (-skip_col_NAME)
- added -v2s_hist option for library history access
* modified Makefile.INCLUDE to put the vol2surf functions in libmri
- added vol2surf.o into CS_OBJS and vol2surf.h into LIBHEADERS
* added vol2surf.[ch] into the src directory (for libmri)
02 September 2004:
* modified 3dROIstats.c to fix the minmax initializer
* modified vol2surf.[ch] SUMA_3dVol2Surf.[ch] (-> v6.1) : library shuffle
09 September 2004:
* added plug_vol2surf.c: for setting the internal volume to surface options
* modified afni_plugin.[ch]: added function PLUTO_set_v2s_addrs()
* modified vol2surf.c
- in afni_vol2surf(), show options on debug
- allow first_node > last_node if last is 0 (default to n-1)
17 September 2004:
* modified SUMA_3dVol2Surf.[ch] (-> v6.2):
- added -gp_index and -reverse_norm_dir options
* modified vol2surf.[ch]: added support for gp_index and altered norm_dir
23 September 2004:
* modified Makefile.linux_gcc33_64 for static Motif under /usr/X11R6/lib64
28 September 2004:
* modified thd_coords.c and 3ddata.h, adding THD_3dmm_to_3dind_no_wod()
04 October 2004:
* added afni_vol2surf.c: for computing SUMA_irgba from v2s_results
* modified afni_niml.c:
- if gv2s_plug_opts.ready, call AFNI_vol2surf_func_overlay()
- use saved_map in case of calling vol2surf twice, identically
- only send nvtot and nvused to suma via AFNI_vnlist_func_overlay()
* modified Makefile.INCLUDE: added afni_vol2surf.o to AFOBJS
* modified plug_vol2surf.c:
- now set global ready if all is well
- clear norms if not in use
- name all local functions PV2S_*
- if debug > 0, display chosen surfaces in terminal
- if debug > 1, display all possible surfaces in terminal
- allow oob and oom values to be arbitrary
- on debug, output complete surface listing in PV2S_check_surfaces()
* modified vol2surf.c:
- added thd_mask_from_brick()
- added compact_results(), in case nalloc > nused
- added realloc_ints() and realloc_vals_list()
- in afni_vol2surf(), if 1 surf and no norms, set steps to 1
- in set_surf_results(), pass gp_index to v2s_apply_filter
- in segment_imarr()
o changed THD_3dmm_to_3dind() to new THD_3dmm_to_3dind_no_wod()
o if THD_extract_series() fails, report an error
- in init_seg_endpoints()
o get rid of p1 and pn
o save THD_dicomm_to_3dmm() until the end
06 October 2004:
* modified afni.h: added AFNI_vol2surf_func_overlay() prototype
* modified afni_niml.c:AFNI_process_niml_data()
- added case for name "SUMA_node_normals" via SUMA_add_norms_xyz()
* modified afni_suma.h: added SUMA_add_norms_xyz() prototype
* modified afni_suma.c: added SUMA_add_norms_xyz() function
* modified SUMA_SurfMeasures.c (->v1.11): to mention 'SurfPatch -vol'
07 October 2004:
* modified afni_plugin.h: fixed extern name PLUTO_set_v2s_addrs()
* modified afni.h: changed prototype for AFNI_vol2surf_func_overlay()
* modified afni_niml.c
- most of the file is part of a diff, beware...
- received local_domain_parent and ID from suma
- added local struct types ldp_surf_list and LDP_list
- in AFNI_process_NIML_data(), broke process_NIML_TYPE blocks out
as separate functions
- added process_NIML_SUMA_node_normals()
- modified AFNI_niml_redisplay_CB() to process surfaces over a list
of local domain parents
- added fill_ldp_surf_list(), to create an LDP list from the surfaces
- added disp_ldp_surf_list(), for debug
* modified afni_vol2surf.c
- new params surfA, surfB, use_defaults for AFNI_vol2surf_func_overlay()
- pass use_defaults to afni_vol2surf()
* modified plug_vol2surf.c
- added second surface pair to globals
- small help and hint changes
- fixed receive order of fr and mm offsets
- verify that surface pairs have matching LDPs
- added PV2S_disp_afni_surfaces() to list all surfaces w/indices
* modified vol2surf.[ch]
- added disp_v2s_plugin_opts()
- dealt with default v2s mapping of surface pairs
- added fill_sopt_default()
- moved v2s_write_outfile_*() here, with print_header()
- in afni_vol2surf(), actually write output files
* modified afni_suma.[ch]
- change idcode_domaingroup to idcode_ldp
- add char label_ldp[64]
- init label_ldp and idcode_ldp
* modified SUMA_3dVol2Surf.[ch] (-> v6.3)
- in suma2afni_surf() deal with LDP changes to SUMA_surface
- changed write_outfile functions to v2s_* and moved them to library
25 October 2004:
* modified afni_niml.c
- use vol2surf for all surfaces now
- so nvused is no longer computed
- in ldp_surf_list, added _ldp suffix to idcode and label
- added full_label_ldp for user clarity
- added functions int_list_posn, slist_choose_surfs,
slist_check_user_surfs and slist_surfs_for_ldp to
handle an arbitrary number of surfaces per LDP
- moved old debug off margin
- pass data/threshold pointers to AFNI_vol2surf_func_overlay()
- pass threshold element with rthresh
- prepare for sending data to suma (but must still define new NIML type)
can get data and global threshold from vol2surf
- for users, try to track actual LDP label in full_label_ldp
- allow absolute thresholding in thd_mask_from_brick()
* modified plug_vol2surf.c
- make sure the surface pairs are actually different
- make sure surfaces have the same number of nodes
- process all parameters, but only complain if "ready"
- always pass along debug/dnode
* modified afni_vol2surf.c:AFNI_vol2surf_func_overlay():
- pass Rdata and Rthr pointers, to optionally return data and thresh
- require absolute thresholding for vol2surf mask
* modified afni.h
- updated AFNI_vol2surf_func_overlay() prototype
* modified vol2surf.c
- apply debug and dnode, even for defaults
- if the user sets dnode, then skip any (debug > 0) tests for it
- check for out of bounds, even if an endpoint is in (e.g. midpoint)
01 November 2004:
* modified nifti1.h, correcting 3 small errors in the descriptions:
- integers from 0 to 2^24 can be represented with a 24 bit mantissa
- we require that a = sqrt(1.0-b*b-c*c-d*d) be nonnegative
- [a,b,0,0] * [0,0,0,1] = [0,0,-b,a]
* modified plug_maxima.[ch]
- remove restrictions on threshold input
- rearrange options, and add a Debug Level
- increment style (should be in {1,2}, not {0,1}
- add a little debug output, including show_point_list_s()
- removed unused variables
- true_max update in find_local_maxima()
- added check for warp-on-demand failure
16 November 2004:
* modified nifti1_io.[ch] nifti1_test.c to include changes from M Jenkinson
- also modified nifti_validfilename, nifti_makebasename and
added nifti_find_file_extension
* added znzlib directory containing config.h Makefile znzlib.[ch]
(unmodified from Mark Jenkinson, except not to define USE_ZLIB)
* modified Makefile.INCLUDE to link znzlib.o into nifti1_test and
with the CS_OBJS in libmri.a
03 December 2004:
* modified nifti1_io.[ch]:
- note: header extensions are not yet checked for
- added formatted history as global string (for printing)
- added nifti_disp_lib_hist(), to display the nifti library history
- added nifti_disp_lib_version(), to display the nifti library version
- re-wrote nifti_findhdrname()
o used nifti_find_file_extension()
o changed order of file tests (default is .nii, depends on input)
o free hdrname on failure
- made similar changes to nifti_findimgname()
- check for NULL return from nifti_findhdrname() calls
- removed most of ERREX() macros
- modified nifti_image_read()
o added debug info and error checking (on gni_debug > 0, only)
o fail if workingname is NULL
o check for failure to open header file
o free workingname on failure
o check for failure of nifti_image_load()
o check for failure of nifti_convert_nhdr2nim()
- changed nifti_image_load() to int, and check nifti_read_buffer return
- changed nifti_read_buffer() to fail on short read, and to count float
fixes (to print on debug)
- changed nifti_image_infodump to print to stderr
- updated function header comments, or moved comments above header
- removed const keyword, changed nifti_image_load() to int, and
added LNI_FERR() macro for error reporting on input files
* modified nifti1_test.c
- if debug, print header and image filenames before changing them
- added -nifti_hist and -nifti_ver options
06 December 2004:
* added list_struct.[ch] to create TYPE_list structures (for nifti, etc.)
(see float_list, for example)
* modified mrilib.h to #include list_struct.h
* modified Makefile.INCLUDE, adding list_struct.o to CS_OBJS
* modified vol2surf.c, changing float_list to float_list_t
10 December 2004: added header extensions to nifti library (v 0.4)
* in nifti1_io.h:
- added num_ext and ext_list to the definition of nifti_image
- made many functions static (more to follow)
- added LNI_MAX_NIA_EXT_LEN, for max nifti_type 3 extension length
* added __DATE__ to version output in nifti_disp_lib_version()
* added nifti_disp_matrix_orient() to print orientation information
* added '.nia' as a valid file extension in nifti_find_file_extension()
* added much more debug output
* in nifti_image_read(), in the case of an ASCII header, check for
* extensions after the end of the header
* added nifti_read_extensions() function
* added nifti_read_next_extension() function
* added nifti_add_exten_to_list() function
* added nifti_valid_extension() function
* added nifti_write_extensions() function
* added nifti_extension_size() function
* in nifti_set_iname_offest():
- adjust offset by the extension size and the extender size
- fixed the 'ceiling modulo 16' computation
* in nifti_image_write_hdr_img2():
- added extension writing
- check for NULL return from nifti_findimgname()
* include number of extensions in nifti_image_to_ascii() output
* in nifti_image_from_ascii():
- return bytes_read as a parameter, computed from the final spos
- extract num_ext from ASCII header
11 Dec 2004:
* added a description of the default operation to the Help in plug_vol2surf.c
14 Dec 2004: added loading a brick list to nifti1 library (v 0.5)
* added nifti_brick_list type to nifti1_io.h, along with new prototypes
* added main nifti_image_read_bricks() function, with description
* added nifti_image_load_bricks() - library function (requires nim)
* added valid_nifti_brick_list() - library function
* added free_NBL() - library function
* added update_nifti_image_for_brick_list() for dimension update
* added nifti_load_NBL_bricks(), nifti_alloc_NBL_mem(),
nifti_copynsort() and force_positive() (static functions)
* in nifti_image_read(), check for failed load only if read_data is set
* broke most of nifti_image_load() into nifti_image_load_prep()
15 Dec 2004: (v 0.6) added writing a brick list to nifti library, and
and nifti library files under a new nifti directory
* modified nifti1_io.[ch]:
- nifti_read_extensions(): print no offset warning for nifti_type 3
- nifti_write_all_data():
o pass nifti_brick_list * NBL, for optional writing
o if NBL, write each sub-brick, sequentially
- nifti_set_iname_offset(): case 1 must have sizeof() cast to int
- pass NBL to nifti_image_write_hdr_img2(), and allow NBL or data
- added nifti_image_write_bricks() wrapper for ...write_hdr_img2()
- prepared for compression use
* modified Makefile.INCLUDE to use nifti directory (and for afni_src.tgz)
* renamed znzlib directory to nifti
* moved nifti1.h, nifti1_io.c, nifti1_io.h and nifti1_test.c under nifti
* modified thd_analyzeread.c and thd_niftiread.c: nifti1_io.h is under nifti
16 Dec 2004:
* moved nifti_stats.c into the nifti directory
* modified Makefile.INCLUDE to compile nifti_stats from the nifti dir
* nifti1.io.[ch] (v 0.7): minor changes to extension reading
21 Dec 2004: nifti library update (v 0.8)
* in nifti_image_read(), compute bytes for extensions (see remaining)
* in nifti_read_extensions(), pass 'remain' as space for extensions,
pass it to nifti_read_next_ext(), and update for each one read
* in nifti_valid_extension(), require (size <= remain)
* in update_nifti_image_brick_list(), update nvox
* in nifti_image_load_bricks(), make explicit check for nbricks <= 0
* in int_force_positive(), check for (!list)
* in swap_nifti_header(), swap sizeof_hdr, and reorder to struct order
* change get_filesize functions to signed ( < 0 is no file or error )
* in nifti_valid_filename(), lose redundant (len < 0) check
* make print_hex_vals() static
* in disp_nifti_1_header, restrict string field widths
23 Dec 2004: nifti library update (v 0.9) - minor updates
* broke ASCII header reading out of nifti_image_read(), into new
functions has_ascii_header() and read_ascii_image()
* check image_read failure and znzseek failure
* altered some debug output
* nifti_write_all_data() now returns an int
29 Dec 2004: nifti library update (v 0.10)
* renamed nifti_valid_extension() to nifti_check_extension()
* added functions nifti_makehdrname() and nifti_makeimgname()
* added function valid_nifti_extensions()
* in nifti_write_extensions(), check for validity before writing
* rewrote nifti_image_write_hdr_img2():
- set write_data and leave_open flags from write_opts
- add debug print statements
- use nifti_write_ascii_image() for the ascii case
- rewrote the logic of all cases to be easier to follow
* broke out code as nifti_write_ascii_image() function
* added debug to top-level write functions, and free the znzFile
* removed unused internal function nifti_image_open()
* modified Makefiles for optional zlib compilation
on: Makefile.linux_gcc32, Makefile.linux_gcc33_64, Makefile.macosx_10.3_G5
off: Makefile.linux_glibc22 Makefile.macosx_10.2, Makefile.macosx_10.3,
Makefile.solaris29_suncc, Makefile.solaris9_suncc_64, Makefile.BSD,
Makefile.darwin, Makefile.cygwin, Makefile.FreeBSD, Makefile.linuxPPC,
Makefile.sgi10k_6.5, Makefile.sgi10k_6.5_gcc, Makefile.sgi5k_6.3,
Makefile.solaris28_gcc, Makefile.solaris28_suncc, Makefile.solaris_gcc,
Makefile.sparc5_2.5, Makefile.sparky, Makefile.sunultra
30 Dec 2004: nifti library and start of nifti_tool
* modified nifti/nifti1_io.[ch] (library v 1.11)
- moved static function prototypes from header to C file
- free extensions in nifti_image_free()
* added nifti/nifti_tool.[ch] (v 0.1) for new program, nifti_tool
* modified Makefile.INCLUDE to compile nifti_tool
* modified nifti/Makefile to compile nifti_stats nifti_tool and nifti1_test
03 Jan 2005:
* modified mri_read.c:mri_imcount() to check for ':' after "3D"
04 Jan 2005:
* afni_niml.c to allow changing the nodes for a surface, made receive
message default to the terminal window
* added a description of AFNI_SHOW_SURF_POPUPS in README.environment
07 Jan 2005: INITIAL RELEASE OF NIFTI LIBRARY (v 1.0)
* added function nifti_set_filenames()
* added function nifti_read_header()
* added static function nhdr_looks_good()
* added static function need_nhdr_swap()
* exported nifti_add_exten_to_list symbol
* fixed #bytes written in nifti_write_extensions()
* only modify offset if it is too small (nifti_set_iname_offset)
* added nifti_type 3 to nifti_makehdrname and nifti_makeimgname
* added function nifti_set_filenames()
* nifti library release 1.1: swap header in nifti_read_header()
07 Jan 2005: INITIAL RELEASE OF nifti_tool (v 1.0)
* lots of functions
* modified Makefile.INCLUDE to compile nifti_test, nifti_stats and
nifti1_test automatically
11 Jan 2005:
* modified afni_niml.c: slist_choose_surfs() check_user_surfs on nsurf == 1
14 Jan 2005: nifti_tool v1.1:
* changed all non-error/non-debug output from stderr to stdout
note: creates a mismatch between normal output and debug messages
* modified act_diff_hdrs and act_diff_nims to do the processing in
lower-level functions
* added functions diff_hdrs, diff_hdrs_list, diff_nims, diff_nims_list
* added function get_field, to return a struct pointer via a fieldname
* made 'quiet' output more quiet (no description on output)
* made hdr and nim_fields arrays global, so do not pass in main()
* return (from main()) after first act_diff() difference
21 Jan 2005:
* modified Makefile.INCLUDE per the request of Vinai Roopchansingh,
adding $(IFLAGS) to the CC line for compiling whereami
* submitted the updated plug_permtest.c from Matthew Belmonte
10 Feb 2005:
* modified nifti1.h and nifti1_io.[ch] for Kate Fissell's doxygen updates
* modified nifti1.h: added doxygen comments for extension structs
* modified nifti1_io.h: put most #defines in #ifdef _NIFTI1_IO_C_ block
* modified nifti1_io.c:
- added a doxygen-style description to every exported function
- added doxygen-style comments within some functions
- re-exported many znzFile functions that I had made static
- re-added nifti_image_open (sorry, Mark)
- every exported function now has 'nifti' in the name (19 functions)
- made sure every alloc() has a failure test
- added nifti_copy_extensions function, for use in nifti_copy_nim_info
- nifti_is_gzfile: added initial strlen test
- nifti_set_filenames: added set_byte_order parameter option
(it seems appropriate to set the BO when new files are associated)
- disp_nifti_1_header: prints to stdout (a.o.t. stderr), with fflush
* modified thd_niftiread.c to call nifti_swap_Nbytes (nifti_ is new)
14 Feb 2005:
* modified plug_maxima.[ch]:
- added 'Sphere Values' and 'Dicom Coords' interface options
16 Feb 2005:
* modified 3dROIstats, added the -mask_f2short option
23 Feb 2005:
* merged Kate's, Mark's and my own nifti code, and made other revisions
* removed contents of nifti directory, and re-created it with the source
tree from sourceforge.net
* modified Makefile.INCLUDE to deal with the new nifti directories
* modified thd_analyzeread.c and thd_niftiread.c not to use include directories
- they now have explicit targets in Makefile.INCLUDE
07 Mar 2005:
* modified thd_coords.c: added THD_3dind_to_3dmm_no_wod()
* modified 3ddata.h: added THD_3dind_to_3dmm_no_wod declaration
* modified plug_maxima.[ch]:
- output appropriate coords via new THD_3dind_to_3dmm_no_wod()
- added new debug output
- changed default separation to 4 voxels
- added gr_fac for printing data values in debug mode
08 Mar 2005:
* modified nifti1_io.[ch], adding global options struct, and optional
validation in nifti_read_header()
* modified nifti_tool.c to remove validation of nifti_1_header structs
17 Mar 2005:
* modified 3dROIstats.c to properly check for failure to use -mask option
21 Mar 2005:
* updated nifti tree with Kate's changes (to fsliolib, mostly)
22 Mar 2005:
* removed all tabs from these files:
- vol2surf.[ch] rickr/3dresample.c rickr/file_tool.[ch]
- plug_crender.c plug_vol2surf.c
- rickr/Imon.[ch] rickr/realtime.[ch] rickr/r_idisp.[ch]
- rickr/r_misc.[ch] rickr/r_new_resam_dset.[ch] rickr/serial_helper.c
- SUMA/SUMA_3dSurf2Vol.[ch] SUMA/SUMA_3dVol2Surf.[ch]
24 March 2005:
* modified strblast.c: added -help, -new_char, -new_string, -unescape options
05 April 2005: NIFTI changes also uploaded at sourceforge.net
* modified nifti/nifti1_io.[ch]
- added nifti_read_collapsed_image(), an interface for reading partial
datasets, specifying a subset of array indices
- for read_collapsed_image, added static functions: rci_read_data(),
rci_alloc_mem(), and make_pivot_list()
- added nifti_nim_is_valid() to check for consistency (more to do)
- added nifti_nim_has_valid_dims() to do many dimensions tests
* modified nifti/Makefile: removed escaped characters, added USEZLIB defn.
* modified nifti/niftilib/Makefile: added nifti1_io.o target, for USEZLIB
* modified nifti/znzlib/Makefile: removed USEZLIB defn.
* modified nifti/utils/nifti_tool.c: (v 1.5) cannot mod_hdr on gzipped file(s)
06 April 2005:
* modified thd_niftiread.c to set ADN_datum with any ADN_ntt or ADN_nvals
* modified edt_dsetitems.c to init new brick types to that of sub-brick 0,
in the case where a type array is not provided
08 April 2005:
* modified nifti_tool.[ch] (-> v1.6)
- added -cbl: 'copy brick list' dataset copy functionality
- added -ccd: 'copy collapsed dimensions' dataset copy functionality
- added -disp_ts: 'disp time series' data display functionality
- moved raw data display to disp_raw_data()
* modified nifti1_io.[ch] (-> v1.7)
- added nifti_update_dims_from_array() - to update dimensions
- modified nifti_makehdrname() and nifti_makeimgname():
if prefix has a valid extension, use it (else make one up)
- added nifti_get_intlist - for making an array of ints
- fixed init of NBL->bsize in nifti_alloc_NBL_mem() {thanks, Bob}
* modified thd_niftiread.c, thd_writedset.c and afni_pplug_env.c to use
the environment variable AFNI_NIFTI_DEBUG
* modified README.environment for AFNI_NIFTI_DEBUG
14 April 2005:
* modified nifti/Makefile: mention 'docs' dir, not 'doc'
* modified nifti/utils/Makefile: added -Wall to nifti_tool build command
* modified nifti/niftilib/nifti1.h: doxygen comments for extension fields
* modified nifti/niftilib/nifti1.[ch] (-> v1.8)
- added nifti_set_type_from_names(), for nifti_set_filenames()
(only updates type if number of files does not match it)
- added is_valid_nifti_type(), just to be sure
- updated description of nifti_read_collapsed_image() for *data change
(if *data is already set, assume memory exists for results)
- modified rci_alloc_mem() to allocate only if *data is NULL
* modified nt_opts in nifti/utils/niftitool.h: ccd->cci, dts_lines->dci_lines,
ccd_dims->ci_dims, and added dci (for display collapsed image)
* modified nifti/utils/niftitool.[ch] (-> v1.7)
- added -dci: 'display collapsed image' functionality
- modified -dts to use -dci
- modified and updated the help in use_full()
- changed copy_collapsed_dims to copy_collapsed_image, etc.
- fixed problem in disp_raw_data() for printing NT_DT_CHAR_PTR
- modified act_disp_ci():
o was act_disp_ts(), now displays arbitrary collapsed image data
o added missed debug filename act_disp_ci()
o can now save free() of data pointer for end of file loop
- modified disp_raw_data()
o takes a flag for whether to print newline
o trailing spaces and zeros are removed from printing floats
- added clear_float_zeros(), to remove trailing zeros
19 April 2005:
* modified nifti1_io.[ch] (-> v1.9) :
- added extension codes NIFTI_ECODE_COMMENT and NIFTI_ECODE_XCEDE
- added nifti_type codes NIFTI_MAX_ECODE and NIFTI_MAX_FTYPE
- added nifti_add_extension() {exported}
- added nifti_fill_extension() as a static function
- added nifti_is_valid_ecode() {exported}
- nifti_type values are now NIFTI_FTYPE_* file codes
- in nifti_read_extensions(), decrement 'remain' by extender size, 4
- in nifti_set_iname_offset(), case 1, update if offset differs
- only output '-d writing nifti file' if debug > 1
* modified nifti_tool.[ch] (-> v1.8) :
- added int_list struct, and keep_hist, etypes & command fields to nt_opts
- added -add_comment_ext action
- allowed for removal of multiple extensions, including option of ALL
- added -keep_hist option, to store the command as a COMMENT extension
(includes fill_cmd_string() and add_int(), is done for all actions)
- added remove_ext_list(), for removing a list of extensions by indices
- added -strip action, to strip all extensions and descrip fields
28 April 2005:
* checked in Kate's changes to fsl_api_driver.c and fslio.[ch]
30 April 2005:
* modified whereami.c so that it does not crash on missing TTatlas+tlrc
05 May 2005:
* modified nifti1_io.h: fixed NIFTI_FTYPE_ASCII (should be 3, not 2)
* modified nifti1_io.c: to incorporate Bob's new NIFTI_SLICE_ALT_INC2
and NIFTI_SLICE_ALT_DEC2 codes from nifti1.h
06 May 2005: Dimon (v 0.1)
* added files for Dimon: Dimon.[ch], dimon_afni.c, l_mri_dicom_hdr.c
* modified Imon.[ch], l_mcw_glob.[ch], rickr/Makefile, Makefile.INCLUDE
* mostly as a check-in for now, details and updates to follow
10 May 2005: nifti fix, Dimon (v 0.2)
* added Kate's real_easy/nifti1_read_write.c to AFNI CVS
* modified znzlib.c, using gzseek() for the failing gzrewind()
* modified nifti_io.c, opening in compressed mode only on '.gz'
* modified to3d.c: fixed help on 'seqplus' and 'seqminus'
* modified plug_realtime.c to handle TPATTERN command for slice timing
* modified Dimon.c, Imon.h: added pause option to opts struct
* modified realtime.c to set TPATTERN from opts.sp (for now)
* modified Makefile.INCLUDE, rickr/Makefile: Dimon depends on Imon.h
17 May 2005: Dimon update (v 0.3)
* modified Dimon.c:
- added -infile_pattern for glob option
- set ftype based on usage
* modified Imon.c, setting ftype
* modified Imon.h, adding IFM_IM_FTYPE_* codes
* modified rickr/realtime.c, base XYZFIRST on ftype, added orient_side_rai()
* modified plug_realtime.c, adding REG_strings_ENV (' ' -> '_')
18 May 2005: Dimon (v 0.4)
* update complete_orients_str() for IFM_IM_FTYPE_DICOM
02 June 2005: 3dVol2Surf (v 6.4)
* added -skip_col_non_results option
08 June 2005: added 2 million to LBUF in mri_read.c (will revisit)
10 June 2005: minor updates to plug_roiedit.[ch]
22 June 2005: Dimon (v 0.5)
* modified Dimon.c: added -infile_prefix option and allowed single volume run
* modified mri_dicom_hdr.c, rickr/l_mri_dicom_hdr.c: fixed small memory leak
23 June 2005:
* modified Makefile.linux_gcc32 and Makefile.linux_gcc33_64
- removed -DNO_GAMMA (was just a warning, but is an error on FC4)
29 June 2005:
* modified nifti1_io.[ch]: changed NIFTI_ECODE_UNKNOWN to _IGNORE
30 June 2005: Dimon (v 0.6)
* modified Dimon.c to process run of single-slice volumes
* modified afni_splash.c and afni_version.c to compile under cygwin
05 July 2005: Dimon (v 1.0 initial release!), Imon (v 3.4)
* modified Dimon.c (-> v 0.7), Imon.[ch]: removed all tabs
* modified Dimon.c: updated -help
* modified Makefile.INCLUDE: include Dimon as part of automatic build
07 July 2005:
* modified rickr/Makefile and Makefile.INCLUDE for the Dimon build
on solaris machines with gcc
13 July 2005: Dimon (v 1.1)
* modified rickr/Dimon.c to handle a run of only 1 or 2 slices, total
22 July 2005:
* modified 3dANOVA2.c 3dANOVA.c 3dclust.c 3dIntracranial.c 3dNotes.c
- Peggy updated the -help output
* modified 3ddelay.c: check for NULL strings before printing
* modified realtime.c (and Dimon.c ->v1.2) to use IOCHAN_CLOSENOW()
25 July 2005:
* modified Dimon.c (-> v1.3): explicit connection close on ctrl-c
27 July 2005:
* submitted Peggy's 3dcalc.c updates (for help)
01 August 2005: Dimon 2.0
* modified Dimon.c, dimon_afni.c, Imon.c
- added the option '-dicom_org' to organize DICOM files before any
other processing
- enabled '-GERT_Reco2', to create a script to build AFNI datasets
02 August 2005:
* modified 3dANOVA2.c, updated calculation of sums of squares for all
a contrasts (including amean and adiff) [rickr, gangc]
03 August 2005:
* modified 3dresample.c, r_new_resam_dset.c, to allow dxyz to override
those from a master (if both are supplied)
17 August 2005: (niftilib -> v1.12)
* incorporated Kate's niftilib-0.2 packaging (v1.11)
* updated comments on most functions, added nifti_type_and_names_match()
22 August 2005:
* modified to3d.c:T3D_set_dependent_geometries, case of not IRREGULAR:
only use fov if nx == ny
23 August 2005: (Dimon -> v2.1)
* added option -sort_by_num_suffix (for Jerzy)
* output TR (instead of 0) in GERT_Reco script (for Peggy)
24 August 2005:
* modified 3dRegAna.c: check for proper ':' usage in -model parameters
25 August 2005: nifti changes for Insight
(nifti_tool -> v1.9, niftilib -> v1.13)
* added CMakeLists.txt in every directory (Hans)
* added Testing/niftilib/nifti_test.c (Hans)
* removed tabs from all *.[ch] files
* modified many Makefiles for SGI test and RANLIB (Hans)
* added appropriate const qualifiers for func param pointers to const data
* modified nifti_io.c, nifti1_test.c, nifti_tool.c, reducing constant
strings below 509 bytes in length (-hist, -help strings)
* modified nifti_stats.c: replaced strdup with malloc/strcpy for warning
29 August 2005: Dimon (-> v 2.2): added options -rev_org_dir and -rev_sort_dir
01 September 2005:
* modified 3dANOVA2.c (to properly handle multiple samples)
* modified Dimon.c/Imon.h (Dimon -> v2.3): added option -tr
13 September 2005:
* modified edt_emptycopy.c, editvol.h
- added functions okay_to_add_markers() and create_empty_marker_set()
* modified 3drefit.c
- moved marker test and creation to said functions in edt_emptycopy.c
* modified plug_realtime.c: add empty markers to appropriate datasets
20 September 2005: modified 2dImReg.c to return 0 from main
26 September 2005:
* modified 3dANOVA3.c: applied formulas provided by Gang for variance
computations of type 4 and 5, A and B contrasts (including means, diffs
and contrs)
04 October 2005:
* checking in changes by Hans Johnson
- added new files Clibs/DartConfig.cmake
- updates to Testing/niftilib/niti_test.c (this is not all ANSI C - fix)
- znzlib.c: cast away const for call to gzwrite
- nifti1_io.c: comment nifti_valid_filename
added nifti_is_complete_filename
added 2 free()s in nifti_findhdrname
cast away const in call to znzwrite
fixed error in QSTR() defn (intent_name[ml]=0 -> nam[ml]=0)
11 October 2005:
* added program 3dmaxima, with files 3dmaxima.c and maxima.[ch]
* plug_maxima.so is now built from plug_maxima.c and maxima.[ch]
* modified Makefile.INCLUDE, adding 3dmaxima to PROGRAMS, adding a
3dmaxima target, and a plug_maxima.so target (for maxima.o)
17 October 2005:
* modified 3dANOVA3.c - added -aBcontr and -Abcontr as 2nd order contrasts
* modified 3dANOVA.h, 3dANOVA.lib - added and initialized appropriate fields
27 October 2005:
* modified 3dANOVA3.c
- fixed -help typo, num_Abcontr assignment and df in calc_Abc()
28 October 2005:
* niftilib update: merged updates by Hans Johnson
- nifti1_io.c:nifti_convert_nhdr2nim : use nifti_set_filenames()
- updated Testing/niftilib/nifti_test.c with more tests
02 November 2005:
* modified nifti1_io.[ch]: added skip_blank_ext to nifti_global_options
- if skip_blank_ext and no extensions, do not read/write extender
04 November 2005:
* modified SUMA_Surface_IO.c:SUMA_2Prefix2SurfaceName() to return NOPE in
exists if exist1 and exist2 are false
07 November 2005:
* checked in rhammett's mri_read_dicom.c changes for the Siemens mosaic format
10 November 2005:
* modified mri_dicom_hdr.h
- In defining LONG_WORD, it was assumed that long was 4 bytes, but this
is not true on 64-bit solaris. Since it was figured out in defining
U32, just use that type for l.
18 November 2005:
* modified nifti1_io.c (nifti_hist -> v1.16):
- removed any test or access of dim[i], i>dim[0]
(except setting them to 0 upon reading, so garbage does not propagate)
- do not set pixdim for collapsed dims to 1.0, leave them
- added magic and dim[i] tests in nifti_hdr_looks_good()
* modified nifti_tool.[ch] (-> v1.10)
- added check_hdr and check_nim action options
* checked in some of Hans' changes (with some alterations)
- a few casts in fslio.[ch] and nifti1_io.[ch] and () in nifti_stats.c
22 November 2005:
* modified 3dANOVA3.c, 3dANOVA.h, 3dANOVA.lib
- added -old_method option for using the a/bmeans, a/bdiff, a/bcontr
computations that assume sphericity (not yet documented)
23 November 2005:
* modified 3dANOVA2.c, added -old_method for type 3 ameans, adiff, acontr
25 November 2005: modified 3dANOVA.c, added subject ethel to -help example
29 November 2005: modified 3dROIstats.c, added more help with examples
02 December 2005:
* modified 3dANOVA3.c, 3dANOVA2.c, 3dANOVA.h, 3dANOVA.lib
- Note updates at the web site defined by ANOVA_MODS_LINK
- The -old_method option requires -OK.
- Added the -assume_sph option and a check for validity of the contrasts.
- Contrasts are verified via contrasts_are_valid().
* fixed Makefile.INCLUDE (had extra '\' at end of PROGRAMS)
08 December 2005: modified 3dRegAna.c, setting default workmem to 750 (MB)
09 December 2005:
* modified 3dANOVA.c
- modified contrast t-stat computations (per Gang)
- added -old_method, -OK, -assume_sph and -debug options
* modified 3dANOVA.h, added debug field to anova_options
* modified 3dANOVA.lib
- no models to check for level 1 in old_method_applies()
- option -OK is insufficient by itself
14 Dec 2005:
* modified edt_coerce.c, added EDIT_convert_dtype() and is_integral_data()
* modified 3dttest.c
- process entire volume at once, not in multiple pieces
- added -voxel option (similar to the 3dANOVA progs)
- replaced scaling work with EDIT_convert_dtype() call
15 Dec 2005: modified 3dhistog.c: fixed use of sub-brick factors
16 Dec 2005: modified 3dUniformize.c: fixed upper_limit==0 case in resample()
28 Dec 2005:
* modified 3dANOVA3.c
- Added -aBdiff, -Abdiff and -abmean options and routines.
- Replaced calc_mean_sum2_acontr() with calc_type4_acontr(), to
avoid intermediate storage of data as floats (by absorbing the
calculate_t_from_sums() operation).
- Similarly, replaced calc_mean_sum2_bcontr() with calc_type4_bcontr().
- Removed calculate_t_from_sums().
- Do checks against EPSILON before sqrt(), in case < 0.
* modified 3dANOVA.h, adding aBdiff, Abdiff and abmean fields to
anova_options struct, along with the ANOVA_BOUND() macro.
* modified 3dANOVA.lib, to init aBdiff, Abdiff and abmean struct members.
29 Dec 2005:
* modified Dimon.c
- make any IMAGE_LOCATION/SLICE_LOCATION difference only a warning
* modified Makefile.INCLUDE (for cygwin)
- removed plug_maxima.fixed from PLUGIN_FIXED
- added Dimon.exe target
* modified fixed_plugins.h: removed plugin_maxima from file
04 Jan 2006:
* modified 3dANOVA2.c, replaced calc_sum_sum2_acontr and calc_t_from_sums
with calc_type3_acontr, to avoid intermediate storage of data as floats
06 Jan 2006: modified waver.c: only output version info with new '-ver' option
25 Jan 2006:
* added model_michaelis_menton.c model function for Jasmin Salloum
* modified NLfit_model.h, added NL_get_aux_filename and NL_get_aux_val protos
* modified 3dNLfim.c, added options -aux_name, -aux_fval and -voxel_count.
* modified Makefile.INCLUDE, added model_michaelis_menton to models target
* modified mri_read.1D: mri_read_ascii to allow 1x1 image file
30 Jan 2006:
* modified model_michaelis_menton.c to get aux info via environment vars
(AFNI_MM_MODEL_RATE_FILE and AFNI_MM_MODEL_DT)
* modified NLfit_model.h and 3dNLfim.c, removing -aux_ options and code
31 Jan 2006:
* modified 3dANOVA3.c, actually assign df_prod, and fix label for aBdiff
* modified nifti_tool.c, check for new vox_offset in act_mod_hdrs
* modified afni_plugout.c, applied (modified) changes by Judd Storrs to
override BASE_TCP_CONTROL with environment variable AFNI_PLUGOUT_TCP_BASE
* modified README.environment for description of AFNI_PLUGOUT_TCP_BASE
02 Feb 2006: submitted version 7 of plug_permtest.c for Matthew Belmonte
07 Feb 2006: added -datum option to 3dWavelets.c
09 Feb 2006: added example to 3dANOVA3 -help
02 Mar 2006:
* modified nifti_tool.c (v 1.12) to deal with nt = 0 in act_cbl(), due
to change of leaving nt..nw as 0 (potentially) in nifti1_io.c
* modified nifti1_io.c (v 1.18) to deal with nt = 0 in nifti_alloc_NBL_mem()
* modified thd_niftiread.c to be sure that ntt and nbuc are at least 1
09 Mar 2006: modified waver.c not to show -help after command typo
13 Mar 2006:
* added examples to 3dmaskave.c
* modified to3d.c, mri_read_dicom.c, mrilib.h: added option and global
variable for assume_dicom_mosaic, to apply the liberal DICOM mosaic test
only when set (via -assume_dicom_mosaic in to3d)
23 Mar 2006: modified 3dcalc.c: do not scale shorts if values are {0,1}
27 Mar 2006:
* modified model_michaelis_menton.c to handle '-time' option to 3dNLfim
* modified 3dmaskdump.c: to keep -quiet quiet
28 Mar 2006: modified vol2surf.c, plug_vol2surf.c: fixed mode computation
28 Mar 2006: modified model_michaelis_menton.c: added mag(nitude) parameter
04 Apr 2006:
* modified cox_render.c
- CREN_set_rgbmap(): if ncol>128, still apply 128 colors
- in BECLEVER sections, enclose bitwise and operations in
parentheses, as '!=' has higher priority than '&'
* modified plug_crender.c
- RCREND_reload_func_dset(): use 128 instead of NPANE_BIG to set
bdelta, and to apply RANGE to bindex (127)
- rd_disp_color_info(), don't assume 128 colors, use NPANE_BIG
06 Apr 2006:
* modified thd_writenifti.c
- in THD_write_nifti, catch populate_nifti_image() failure (crashed)
- in populate_nifti_image(), return NULL (not 0) on failure, and give
a hint for what to do in case of 'brick factors not consistent'
11 Apr 2006: put 'd' in 3dANOVA* 'Changes have been made' warnings
14 Apr 2006: applied mastery to NIFTI-1 datasets
* modified thd_mastery.c:
- allow NIfTI suffices in THD_open_dataset()
- if NIfTI, init master_bot and master_top
* modified thd_load_datablock.c: broke sub-ranging out to
THD_apply_master_subrange() for use in THD_load_nifti()
* modified 3ddata.h: added prototype for THD_apply_master_subrange()
* modified thd_niftiread.c: THD_load_nifti():
- if mastered, pass nvals and master_ival to nifti_image_read_bricks()
- at end, if mastered and bot <= top, THD_apply_master_subrange()
18 Apr 2006:
* modified cs_addto_args.c: addto_args(), terminate empty sin before strcat
* modified mri_matrix.c: moved var defn to start of block in DECODE_VALUE
* modified SUMA_3dSkull_Strip.c: 'int code[3]' must be defined at block start
19 Apr 2006: nifticlib-0.3 updates (from Kate Fissell)
* added Updates.txt
* modified Makefile, utils/Makefile: removed $(ARCH) and commented SGI lines
* modified real_easy/nifti1_read_write.c : corrected typos
* modified 3dcalc.c: fixed typo in 'step(9-(x-20)*...' example
20 Apr 2006:
* modified thd_opendset.c: added functions storage_mode_from_filename()
and has_known_non_afni_extension() {for 3dcopy}
* modified 3ddata.h: added prototypes for those two functions
21 Apr 2006: modified model_michaelis_menton.c: apply AFNI_MM_MODEL_RATE_IN_SECS
24 Apr 2006: nifti_tool.c:act_disp_ci(): removed time series length check
25 Apr 2006: changed ^M to newline in 3dcopy.c (stupid Macs)
28 Apr 2006: 3dhistog.c: fixed min/max range setting kk outside array
08 May 2006: 3drefit.c: added options -shift_tags, -dxtag, -dytag, -dztag
17 May 2006:
* modified mri_dicom_hdr.c, rickr/l_mri_dicom_hdr.c
- make reading of preamble automatic
- do not print any 'illegal odd length' warnings
18 May 2006: allowed for older DICOM files that do not have a preamble
* removed rickr/l_mri_dicom_hdr.c
* modified mri_dicom_hdr.c
- added FOR_DICOM test to compile for Dicom
- made g_readpreamble global, set in DCM_OpenFile, used in readFile1
- DCM_OpenFile reads 132 bytes to check for "DICM" at end
* modified rickr/Makefile to use ../mri_dicom_hdr.c aot l_mri_dicom_hdr.c
23 May 2006: some nifti updates by Hans Johnson (lib ver 1.19)
* added Testing/Data, /Testing/niftilib/nifti_test2.c and
Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz
* modified CMakeLists.txt, niftilib/CMakeLists.txt, utils/CMakeLists.txt,
Testing/niftilib/nifti_test.c
* modified utils/nifti_stats.c: added switch for not building unused funcs
* modified nifti1_io.c:
- nifti_write_ascii_image(): free(hstr)
- nifti_copy_extensions(): clear num_ext, ext_list
* rickr: use NULL when clearing ext_list
26 May 2006: .niml/.niml.dset preparations
* modified 3ddata.h
- #define STORAGE_BY_NIML,NI_SURF_DSET, and update LAST_STORAGE_MODE
- add nnodes, node_list to THD_datablock struct
- define DBLK_IS_NIML, DBLK_IS_NI_SURF_DSET, and similar DSET_*
* modified thd_open_dset.c:
- THD_open_one_dataset(): added (unfinished) .niml/.niml.dset cases
- storage_mode_from_filename(): added .niml/.nim.dset cases
* modified thd_info.c: THD_dataset_info(): added the 2 new STORAGE_MODEs
* modified thd_loadblk.c: added (unfinished) cases for the new storage modes
30 May 2006:
* modified 3dclust.c: get a new ID for an output 3dclust dataset
* modified Imon.h, Dimon.c: added -save_file_list option
15 Jun 2006:
* modified thd_niftiwrite.c:
- in populate_nifti_image(), check for including any adjacent zero offset
in the slice timing pattern
- added get_slice_timing_pattern() to test for NIFTI_SLICE_* patterns
20 Jun 2006: modified 3drefit.c to handle NIfTI datasets
21 Jun 2006:
* modified niml.h, niml_util.c: added NI_strdup_len()
* modified @make_stim_file, adding -zero_based option
27 Jun 2006:
* modified nifti1_io.c: fixed assign of efirst to match stated logic in
nifti_findhdrname() (problem found by Atle Bjørnerud)
28 Jun 2006: many changes to handle NIML and NI_SURF_DSET datasets (incomplete)
* added thd_niml.c
- top-level THD_open_niml(), THD_load_niml(), THD_write_niml() functions
- general read_niml_file(), write_niml_file() functions
- processing NI_SURF_DSET datasets, including THD_ni_surf_dset_to_afni()
* modified thd_opendset.c
- added file_extension_list array and find_filename_extension()
- apply THD_open_niml() to NIML and NI_SURF_DSET cases
* modified 3ddata.h - added prototypes
* modified edt_dset_items.c: added DSET_IS_NIML, DSET_IS_NI_SURF_DSET cases
for new_prefix editing
* modified thd_3Ddset.c
- broke THD_open_3D() into read_niml_file() and THD_niml_3D_to_dataset()
* modified thd_fetchdset.c
- added NIML and NI_SURF_DSET cases
* modified thd_loaddblk.c
- opened STORAGE_BY_NIML and BY_NI_SURF_DSET cases
* modified thd_nimlatr.c: just for unused variables
* modified thd_writedset.c:
- added NIML and NI_SURF_DSET write cases using THD_write_niml()
* modified Makefile.INCLUDE: to add thd_niml.o to THD_OBJS
30 Jun 2006:
* modified SUMA_3dVol2Surf.[ch], vol2surf.[ch], plug_vol2surf.c
- added -save_seg_coords option
07 Jul 2006:
* modified @auto_tlrc: changed 3dMax to 3dBrickStat
11 Jul 2006:
* modified niml_element.c: fixed use of NI_realloc() in NI_search_group_*()
* modified 3ddata.h: changed THD_write_niml to Boolean, added prototypes
for THD_dset_to_ni_surf_dset() and THD_add_sparse_data()
* modified thd_writedset.c:
- don't let NI_SURF_DSET get written as 1D
* modified thd_niml.c:
- added load for NI_SURF_DSET
- added basic write for NI_SURF_DSET
12 Jul 2006:
* modified edt_emptycopy.c: init nnodes and node_list
* modified thd_auxdata.c: for NI_SURF_DSET, copy any nnodes and node_list
* modified thd_delete.c: free dblk->node_list
* modified thd_niml.c: (maybe good enough for SUMA now)
- write out more attributes
- use matching XtMalloc for dblk allocation
* modified 3ddata.h: added THD_[un]zblock_ch protos
* modified thd_zblock.c: added THD_zblock_ch() and THD_unzblock_ch()
14 Jul 2006:
* modified 3ddata.h: added IS_VALID_NON_AFNI_DSET() macro
* modified 3dNotes.c:
- replaced if(DSET_IS_NIFTI()) with if(IS_VALID_NON_AFNI_DSET())
* modified 3drefit.c: same change as 3dNotes.c
* modified 3dniml.c: pass dset to nsd_add_sparse_data for nx
* modified niml_element.c, niml.h
- added NI_set_ni_type_atr() and calls to it from NI_add_column() and
stride(), so if ni_type is already set, it is adjusted
17 Jul 2006:
* modified niml_element.c, niml.h:
- fixed NI_set_ni_type_atr() to allow for type name of arbitrary length,
not just known types
- added NI_free_element_data()
* modified thd_niml.c: added nsd_add_colms_type, to add column types for suma
18 Jul 2006:
* modified thd_niml.c:
- added COLMS_RANGE attribute element
- use AFNI_NI_DEBUG as an integer level (as usual)
28 Jul 2006:
* modified 3drefit.c: fixed saveatr use, and blocked atr mods with other mods
03 Aug 2006: updates for writing niml files as NI_SURF_DSET
* modified thd_niml.c:
- added ni_globals struct to deal with debug and write_mode
- added and used set_ni_globs_from_env() for assigning those globals
- added set_sparse_data_attribs()
- added set/get access functions for globals debug and write_mode
* modified 3dvol2surf.c
- added v2s_write_outfile_NSD(), and use it instead of _niml()
- remove unused code in dump_surf_3dt()
- added static set_output_labels()
- allocate labels array in alloc_output_mem()
- free labels and labels array in free_v2s_results()
* modified 3dvol2surf.h: added labels and nlab to v2s_results struct
* modified SUMA_3dVol2Surf.c: use v2s_write_outfile_NSD, instead of _niml()
* modified 3ddata.h
- added protos for ni_globs functions and set_sparse_data_attribs()
04 Aug 2006: auto-convert NI_SURF_DSET to floats
* modified thd_niml.c:
- added to_float to ni_globals struct, for blocking conversion to floats
- changed LOC_GET_MIN_MAX_POSN to NOTYPE_GET_MIN_MAX_POSN
- added get_blk_min_max_posn(), to deal with varrying input types
- fixed missing output column type when no node_list
- nsd_add_colms_range(): do not require input type to be float
- nsd_add_sparse_data(): convert output to floats, if necessary
- add gni.to_float accessor funcs and in set_ni_globs_from_env()
* modified vol2surf.c: changed set_ni_debug() to set_gni_debug()
* modified 3ddata.h: changed prototype names, and added to_float protos
08 Aug 2006: C++ compilation changes from Greg Balls
* modified niml/niml.h rickr/r_idisp.h rickr/r_new_resam_dset.h 3ddata.h
afni_environ.h afni_graph.h afni.h afni_pcor.h afni_setup.h afni_suma.h
afni_warp.h bbox.h cdflib.h coxplot.h cox_render.h cs.h debugtrace.h
display.h editvol.h imseq.h machdep.c machdep.h maxima.h mcw_glob.h
mcw_graf.h mcw_malloc.h mrilib.h mri_render.h multivector.h parser.h
pbar.h plug_permtest.c plug_retroicor.c retroicor.h thd_compress.h
thd_iochan.h thd_maker.h vol2surf.h xim.h xutil.h
(mostly adding #ifdef __cplusplus extern "C" { #endif, and closing set)
* modified rickr/Makefile: removed ../ge4_header.o from file_tool dep list
09 Aug 2006: vol2surf creation of command history
* modified vol2surf.c:
- create argc, argv from options in v2s_make_command()
- added loc_add_2_list() and v2s_free_cmd() for v2s_make_command()
- added labels, thres index/value and surf vol dset to gv2s_plug_opts
* modified vol2surf.h:
- added v2s_cmt_t struct, and into v2s_opts_t
- added gpt_index/thresh, label and sv_dset to v2s_plugin_opts
* modified afni_niml.c: receive spec file name via surface_specfile_name atr
* modified afni_suma.h: added spec_file to SUMA_surface
* modified afni_vol2surf.c:
- store the surface volume dataset in the v2s_plugin_opts struct
- also store the index and threshold value of the threshold sub-brick
* modified plug_vol2surf.c:
- init surface labels, and set them given the user options
* modified SUMA_3dVol2Surf.c:
- store command-line arguments for history note
- added -skip_col_NSD_format option
* modified SUMA_3dVol2Surf.h:
- added argc, argv to set_smap_opts parameters
* modified edt_empty_copy.c: if they exist, let okay_to_add_markers() return 1
14 Aug 2006:
* modified mri_dicom_hdr.c, setting the type for g_readpreamble
* modified rickr/Makefile: remove dependencies on an ../*.o, so they are
not removed by the build process (they should not be made from rickr)
15 Aug 2006: added Makefile.linux_xorg7
17 Aug 2006:
* modified thd_niml.c: fixed str in loc_append_vals()
* modified Makefile.linux_xorg7: set SUMA_GLIB_VER = -2.0
* modified Makefile.INCLUDE, passed any SUMA_GLIB_VER to SUMA builds
* modified SUMA_Makefile_NoDev, link glib via -lglib${SUMA_GLIB_VER}
* modified Vecwarp.c: fixed matrix-vector screen output (req. by Tom Holroyd)
18 Aug 2006: modified 3dmaxima.c, maxima.[ch]: added -coords_only option
23 Aug 2006:
* modified thd_niml.c:
- added sorted_node_def attr to SPARSE_DATA
- if set_sparse_data_attribs(), if nodes_from_dset, the set
sorted_node_def based on node_list in dset via has_sorted_node_list()
* modified vol2surf.c:
- use -outcols_afni_NSD in v2s_make_command
- in v2s_write_outfile_NSD(), only output node list if it exists
- pass 0 as nodes_from_dset to has_sorted_node_list()
* modified SUMA_3dVol2Surf.c (-> v6.7)
- changed -skip_col_* options to -outcols_* options
- added -outcols_afni_NSD option
* modified 3ddata.h: added nodes_from_dset to set_sparse_data_attribs()
23 Aug 2006: do not assume node index column is #0 in NI_SURF_DSET
* modified thd_niml.c:
- added sum_ngr_get_node_column()
- apply in process_ni_sd_sparse_data(), process_ni_sd_attrs() and
THD_add_sparse_data
* modified vol2surf.c: possibly free nodes during write_NSD
* modified 3ddata.h: added suma_ngr_get_node_column() prototype
25 Aug 2006:
* modified thd_niml.c
- added node_col to ni_globals, and hold the niml node column index
- modified nsd_string_atr_to_slist() to skip a given index
- apply node_col to process_ni_sparse_data() and process_ni_sd_attrs()
- modified THD_add_sparse_data() to omit gni.node_col, not col 0
30 Aug 2006: INDEX_LIST is now a separate attribute element in the group
* modified thd_niml.c:
- updated nsd_string_atr_to_slist(), THD_ni_surf_dset_to_afni(),
process_NSD_sparse_data(), process_NSD_attrs(), THD_add_sparse_data(),
THD_dset_to_ni_surf_dset(), nsd_add_colms_type(),
nsd_add_str_atr_to_group(), nsd_add_colms_range(),
nsd_add_sparse_data(), set_sparse_data_attribs()
- added process_NSD_index_list(), to read INDEX_LIST attribute element
- added nsd_fill_index_list(), to create the INDEX_LIST element
- added NI_get_byte_order(), to process "ni_form" attribute
- removed suma_ngr_get_node_column()
- removed node_col from ni_globals
- modified new nsd_fill_index_list():
add default list when AFNI_NSD_ADD_NODES is set
* modified 3ddata.h: lose suma_ngr_get_node_column(), add NI_get_byte_order()
* added Makefile.linux_xorg7_64 (compiled on radagast)
05 Sep 2006:
* modified nifti1_io.c, added nifti_set_skip_blank_ext
* merged many fslio NIfTI changes by Kate Fissell for niftilib-0.4
* modified thd_niml.c: removed warning about missing Node_Index column type
06 Sep 2006:
* modified vol2surf.c: use NI_free after NI_search_group_shallow
* modified thd_niml.c: in nsd_add_str_atr_to_group() swap out nul chars
* merged small nifti/README change
12 Sep 2006: modified thd_niml.c:THD_open_niml(): set brick_name to fname
15 Sep 2006: modified 3ddata.h: added AFNI_vedit_clear proto (for Greg Balls)
28 Sep 2006:
* modified thd_niml.c:close niml stream in write_niml_file()
* modified afni_niml.c:no AFNI_finalize_dataset_CB from process_NIML_SUMA_ixyz
12 Oct 2006: added serial_writer.c program for rasmus
16 Oct 2006: modified serial_writer.c: added -ms_sleep, -nblocks and -swap
22 Oct 2006: added model_demri_3.c
23 Oct 2006: modified model_demri_3.c with DGlen, 2 speed-ups, 1 negation fix
24 Oct 2006: modified model_demri_3.c: mpc was not stored across iterations
25 Oct 2006:
* modified 3dNLfim.c:
- updated check of proc_shmptr
- change on of the TR uses to TF (computing ct from cp)
- expanded help, and added a sample script
26 Oct 2006:
* modified Makefile.INCLUDE: added $(LFLAGS) to 3dNLfim target
* modified 3dNLfim.c: limit g_voxel_count output to every 10th voxel
: RIB and RIT replace single R
30 Oct 2006: modified afni_base.py: added comopt.required, show(), print mods
31 Oct 2006: modified model_demri_3.c: allow ve param, instead of k_ep
02 Nov 2006: modified model_demri_3.c: change init, so Ve is reported as output
13 Nov 2006: changes to send ROI means to serial_helper (from Tom Ross)
* modified plug_realtime.c:
- added Mask dataset input to plugin interface
- if Mask, send averages over each ROI to AFNI_REALTIME_MP_HOST_PORT
* modified serial_helper.c:
- added -num_extras option to process extra floats per TR (ROI aves)
* modified thd_makemask.c:
- added thd_mask_from_brick() from vol2surf.c
- added new thd_multi_mask_from_brick()
* modified 3dvol2surf.c: moved thd_mask_from_brick() to thd_makemask.c
* modified 3ddata.h: added protos for mask functions
15 Nov 2006: modified serial_helper.c: encode nex into handshake byte
17 Nov 2006:
* modified model_demri_3.c:
- do not exit on fatal errors, complain and return zero'd data
- if model parameters are bad (esp. computed), zero data and return
- if thd_floatscan() on results shows bad floats, zero data and return
- require AFNI_MODEL_D3_R1I_DSET to be float
- removed R1I_data_im
* added afni_util.py, afni_proc.py, make.stim.times.py,
and option_list.py to python_scripts
* modified afni_base.py
18 Nov 2006: small mods to afni_base.py, afni_proc.py, option_list.py
20 Nov 2006:
* modified Dimon.c, dimon_afni.c, Imon.h:
- added -epsilon option for difference tests, including in dimon_afni.c
01 Dec 2006: python updates
* added db_mod.py: contains datablock modification functions (may disappear)
* modified afni_base.py:
- added afni_name:rpv() - to return the relative path, if possible
- added read_attribute(), which calls 3dAttribute on a dataset
* modified afni_proc.py: now does most of the pre-processing
* modified option_list.py:
- added setpar parameter to OptionList:add_opt()
- updated comments
02 Dec 2006: modified suma_datasets.c:
- SUMA_iswordin -> strstr, MAXPATHLEN -> SUMA_MAX_DIR_LENGTH
07 Dec 2006: minor mods to afni_util.py, db_mod.py, make.stim.times.py
09 Dec 2006: 3dDeconvolve command in afni_proc.py
* modified make.stim.times.py, afni_util.py, afni_proc.py, db_mod.py
10 Dec 2006: modified afni_proc.py, db_mod.py: help and other updates
11 Dec 2006: more uber-script updates
* modified afni_proc.py: added version, history and complete help
* modified db_mod.py: volreg_base_ind now takes run number, not dset index
* modified make_stim_times.py:
- renamed from make.stim.times.py
- more help
- per output file, append '*' if first stim row has only 1 stim
* modified vol2surf.[ch]: if plug_v2s:debug > 2, print 3dV2S command
12 Dec 2006:
* modified afni_proc.py, db_mod.py, option_list.py:
- added fitts and iresp options, fixed scale limit
13 Dec 2006:
* modified afni_proc.py, db_mod.py
- added -regress_stim_times_offset and -no_proc_command
(afni_proc commands are stored by default)
* modified make_stim_times.py: added -offset option
14 Dec 2006:
* modified afni_proc.py, db_mod.py
- added -copy_anat, -regress_make_1D_ideal and -regress_opts_3dD
* modified make_stim_times.py: added required -nt option
15 Dec 2006: modified SUMA_3dVol2surf: help for niml.dest and EPI -> surface
17 Dec 2006: modified afni_proc.py, db_mod.py:
- added options -tshift_opts_ts, -volreg_opts_vr, -blur_opts_merge
18 Dec 2006: small mods to afni_proc.py, db_mod.py, make_stim_times.py
19 Dec 2006:
* modified afni_proc.py, db_mod.py: help update, use quotize_list
* modified afni_util.py: added quotist_list
* modified make_stim_times.py: use str(%f) for printing
20 Dec 2006: afni_proc.py (version 1.0 - initial release)
* modified afni_proc.py
- changed -regress_make_1D_ideal to -regress_make_ideal_sum
- added output of stim ideals (default) and option -regress_no_ideals
- verify that AFNI datasets are unique
- added -regress_no_stim_times
* modified afni_base.py: added afni_name.pve()
* modified afni_util.py: added uniq_list_as_dsets, basis_has_known_response
* modified db_mod.py: for change in 'ideal' options & -regress_no_stim_times
* added ask_me.py: basically empty, to prompt users for options
21 Dec 2006: afni_proc.py (v1.2)
- help, start -ask_me, updated when to use -iresp/ideal
22 Dec 2006: modified afni_proc.py, make_stim_times.py for AFNI_data2 times
25 Dec 2006:
* modified afni_proc.py (v1.4): updates for -ask_me
* modified ask_me.py: first pass, result matches ED_process
* modified afni_util.py: added list_to_datasets() and float test
* small mods to db_mod.py, option_list
27 Dec 2006: afni_proc.py (1.5): ask_me help
28 Dec 2006: afni_proc.py (1.6)
* modified afni_proc.py: added -gltsym examples
* modified afni_util.py: added an opt_prefix parameter to quotize_list()
* modified db_mod.py : used min(200,a/b*100) in scale block
03 Jan 2007: afni_proc.py (1.7)
* modified afni_proc.py, afni_util.py, db_mod.py:
- help updates, no blank '\' line from -gltsym, -copy_anat in examples
* modified 3dTshift.c: added -no_detrend
04 Jan 2007: modified 3dTshift.c: added warning for -no_detrend and MRI_FOURIER
08 Jan 2007: afni_proc.py (1.8)
* modified afni_proc.py, db_mod.py:
- changed default script name to proc.SUBJ_ID, and removed -script from
most examples
- added options '-bash', '-copy_files', '-volreg_zpad', '-tlrc_anat',
'-tlrc_base', '-tlrc_no_ss', '-tlrc_rmode', '-tlrc_suffix'
10 Jan 2007: afni_proc.py (1.9) added aligned line wrapping
* modified afni_proc.py, afni_util.py
- new functions add_line_wrappers, align_wrappers, insert_wrappers,
get_next_indentation, needs_wrapper, find_command_end,
num_leading_line_spaces, find_next_space, find_last_space
11 Jan 2007: modified afni_proc.py:
- subj = $argv[1], added index to -glt_label in -help
- rename glt contrast files to gltN.txt (so change AFNI_data2 files)
12 Jan 2007: modified afni_proc.py (1.11), db_mod.py:
- added options -move_preproc_files, -regress_no_motion
- use $output_dir var in script, and echo version at run-time
- append .$subj to more output files
16 Jan 2007:
* modified plug_crender.c: fixed use of Pos with bigmode
* modified db_mod.py to allow -tlrc_anat without a +view in -copy_anat
17 Jan 2007: modified db_mod.py: -tlrc_anat ==> default of '-tlrc_suffix NONE'
26 Jan 2007: modified afni_base.py, afni_proc.py, afni_util.py, ask_me.py
db_mod.py, make_stim_times.py, option_list.py
- changed all True/False uses to 1/0 (for older python versions)
- afni_proc.py: if only 1 run, warn user, do not use 3dMean
02 Feb 2007:
- afni_proc.py: put execution command at top of script
- modified db_mod.py: print blur_size as float
- modified make_stim_times.py: added -ver, -hist, extra '*' run 1 only
06 Feb 2007: added TTatlas example to 3dcalc help
20 Feb 2007:
* modified -help of make_stim_times.c (fixing old make.stim.times)
* modified thd_opendset.c: made fsize unsigned (handles 4.2 GB files, now)
21 Feb 2007: modified afni_proc.py (1.16), db_mod.py
- added optional 'despike' block
- added options -do_block and -despike_opts_3dDes
* updated nifti tree to match that of sourceforge
- minor changes to CMakeLists.txt DartConfig.cmake
examples/CMakeLists.txt niftilib/CMakeLists.txt niftilib/nifti1_io.c
real_easy/nifti1_read_write.c Testing/niftilib/nifti_test.c
utils/CMakeLists.txt znzlib/CMakeLists.txt znzlib/znzlib.h
* updated nifti/fsliolib/fslio.c: NULL check from David Akers
23 Feb 2007:
* modified imseq.c to do tick div in mm for Binder
* modified README.environment: added AFNI_IMAGE_TICK_DIV_IN_MM variable
27 Feb 2007: afni_proc.py (v 1.17)
* modified afni_proc.py, db_mod.py, option_list.py:
-volreg_align_to defaults to 'third' (was 'first')
-added +orig to despike input
-added 'empty' block type, for a placeholder
28 Feb 2007: fixed fsize problem in thd_opendset.c (from change to unsigned)
01 Mar 2007:
* modified README.environment
- added variables AFNI_NIML_DEBUG, AFNI_NSD_ADD_NODES,
AFNI_NSD_TO_FLOAT and AFNI_NIML_TEXT_DATA
* modified thd_niml.c: allowed sub-brick selection via thd_mastery
* modified thd_mastery.c: init master_bot/top for .niml.dset files
02 Mar 2007:
* modified count.c
- added '-sep', same as '-suffix'
- extended number of strncmp() characters for many options
* modified option_list.py: if n_exp = -N, then at least N opts are required
05 Mar 2007: per Jason Bacon and Michael Hanke:
* JB: modified @escape-: added '!' in #!/bin/tcsh
* JB: modified ask_me.py, db_mod.py, added 'env python', for crazy users
* MH: added nifti/nifticdf: CMakeLists.txt, Makefile, nifticdf.c, nifticdf.h
(separating nifti_stats.c into nifticdf.[ch])
* MH: modified CMakeLists.txt and utils/CMakeLists.txt for cmake
* MH: modified nifti_stats.c (removed all functions but main)
* rr: modified Makefile, README, utils/Makefile (to build without cmake)
* rr: modified Makefile.INCLUDE
- replace nifti_stats.o with nifticdf.o in CS_OBJS
- add nifticdf.o target and link to nifti_stats
- modified nifticdf.[ch]: reverted back closer to nifti_stats.c
(moving 7 protos to nifticdf.h, and all but main to nifticdf.c)
(keep all static and __COMPILE_UNUSED_FUNCTIONS__ use)
15 Mar 2007: mod afni_proc.py, db_mod.py: use x1D suffix, removed -full_first
19 Mar 2007: modified afni_proc.py: allow dataset TR stored in depreciated ms
25 Mar 2007: afni_proc.py: added -help for long-existing -regress_no_stim_times
19 Apr 2007: afni_proc.py (v1.21): apply +orig in 1-run mean using 3dcopy
01 May 2007: included Hans' updates: CMakeLists.txt, nifticdf/CMakeLists.txt
03 May 2007:
* added 3dPAR2AFNI.pl, from Colm G. Connolly
* modified Makefile.INCLUDE: added 3dPAR2AFNI.pl to SCRIPTS
* modified afni_proc.py: added BLOCK(5) to the examples
08 May 2007:
* w/dglen, mod 3dcalc.c, thd_mastery.c to handle long sub-brick lists
* modified afni_proc.py, db_mod.py, option_list.py (v 1.22)
- change read_options() to be compatible with python version 2.2
- '-basis_normall 1' is no longer used by default
- rename -regress_no_stim_times to -regress_use_stim_files
10 May 2007:
* modified nifticdf.[ch], mrilib.h, Makefile.INCLUDE, SUMA_Makefile_NoDev
- use cdflib functions from nifticdf, not from cdflib directory
* removed cdflib directory and cdflib.h
16 May 2007:
* modified nifti/Updates.txt in preparation of nifticlib-0.5 release
* modified nifti1_read_write.c for Kate, to fix comment typo
17 May 2007: nifti update for release 0.5
* modified Clibs/CMakeLists.txt, set MINOR to 5
* modified Makefile, examples/Makefile, utils/Makefile to apply ARCH
variable for easier building
30 May 2007: nifti CMakeList updates from Michael Hanke
01 Jun 2007:
* modified afni_proc.py, db_mod.py:
- changed Xmat.1D to X.xmat.1D, apply -xjpeg in 3dDeconvolve
* modified nifti/Makefile, README for nifticlib-0.5 release
04 Jun 2007:
* modified nifti1_io.c: noted release 0.5 in history
* modified nifti_tool.c: added free_opts_mem() to appease valgrind
* modified afni_proc.py, db_mod.py: added -scale_no_max
05 Jun 2007:
* modified nifti1_io.c: nifti_add_exten_to_list:
- revert on failure, free old list
* modified nifti_tool.c: act_check_hdrs: free(nim)->nifti_image_free()
06 Jun 2007:
* modified thd_makemask.c: THD_makemask() and THD_makedsetmask()
- for short and byte datasets, check for empty mask
07 Jun 2007:
* modified nifti1_io.c: nifti_copy_extensions: use esize-8 for data size
* modified nifti1.h: note that edata is of length esize-8
08 Jun 2007:
* modified file_tool.[ch]: added -show_bad_backslash and -show_file_type
11 Jun 2007: updates for new image creation
* modified nifti1_io.[ch]:
- added nifti_make_new_header() - to create from dims/dtype
- added nifti_make_new_nim() - to create from dims/dtype/fill
- added nifti_is_valid_datatype(), and more debug info
* modified nifti_tool.[ch]:
- added nt_image_read, nt_read_header and nt_read_bricks
to wrap nifti read functions, allowing creation of new datasets
- added -make_im, -new_dim, -new_datatype and -copy_im
* modified nifti1_test.c: added trailing nifti_image_free(nim)
* modified thd_niftiread.c: to allow nx = ny = 1
13 Jun 2007: nifti_tool.c help update, file_tool.c help update
22 Jun 2007: modified linux_xorg7 and _64 Makefiles to link motif statically
27 Jun 2007:
* modified afni_base.py, afni_proc.py, afni_util.py, db_mod.py:
- on error, display failed command
* modified Makefile_linux_xorg7 and xorg7_64 for static linking in SUMA
28 Jun 2007: minor changes from HJ
* modified CMakeLists.txt, niftilib/CMakeLists.txt, nifti1_io.c
29 Jun 2007: file_tool can work with ANALYZE headers
* added fields.[ch], incorporating field lists from nifti_tool
* modified file_tool.[ch]:
- added options -def_ana_hdr, -diff_ana_hdrs, -disp_ana_hdr, -hex
* modified rickr/Makefile: file_tool depends on fields.[ch]
* modified 3dANOVA.h: set MAX_OBS to 300, for T. Holroyd
30 Jun 2007: modified Makefile.INCLUDE: added svm to afni_src.tgz target
01 Jul 2007:
* modified fields.[ch]: added add_string (from nifti_tool.c)
* modified file_tool.[ch]: added ability to modify fields of an ANALYZE file
02 Jul 2007:
* modified thd_niftiread.c: changed missing xform error to warning
* modified model_demri_3.c: return on first_time errors
* modified 3dcopy.c: complain and exit on unknown option
03 Jul 2007: modified model_demri_3.c: allow MP file as row
10 Jul 2007: modified thd_coords.c: moved verbose under fabs(ang_merit)
17 Jul 2007: modified 3dmaxima.c: fixed -n_style_sort option use
18 Jul 2007: first GIFTI files added (v 0.0)
* added gifti directory and simple Makefile
* added gifti.[ch] : main programmer library functions
* added gifti_xml.[ch] : XML functions, to be called from gifti.c
* added gtest.[ch] : a sample test of the library files
* added get.times : a script to time reading of gifti images
* added test.io : a script to test GIFTI->GIFTI I/O
* modified Makefile.INCLUDE : to copy gifti directory for afni_src.tgz
19 Jul 2007: modified model_demri_3.c: minor tweak to ct(t) equation
20 Jul 2007: modified Makefile.INCLUDE, gifti/Makefile, for building gtest
24 Jul 2007:
* modified rickr/r_new_resam_dset.[ch] rickr/3dresample.c
SUMA/SUMA_3dSkullStrip.c 3dSpatNorm.c plug_crender.c whereami.c
rickr/Makefile Makefile.INCLUDE SUMA/SUMA_Makefile_NoDev
- removed librickr.a (objects go into libmri.a)
- added get_data param to r_new_resam_dset()
25 Jul 2007:
* modified svm/3dsvm_common.c to use rint (aot rintf (re: solaris))
* modified model_demri_3.c: help update
26 Jul 2007:
* modified Makefile.INCLUDE to not use $< variable
* modified 3dDeconvolve.c: -stim_times with exactly 0 good times is okay
* modified svm/plug_3dsvm.c: moved variable definitions to block tops
* modified Dimon.c, Imon.c: help typos
27 Jul 2007:
* modified nifti1_io.[ch]: handle 1 vol > 2^31 bytes
* modified nifti_tool.c: return 0 on -help, -hist, -ver
* modified thd_niftiwrite.c: replace some all-caps prints
28 Jul 2007:
* modified nifti1_io.[ch]: handle multiple volumes > 2^32 bytes
* modified: 1dSEM.c 2dImReg.c 3dDTtoDWI.c 3dDWItoDT.c 3dNLfim.c
3dStatClust.c 3dTSgen.c 3dUniformize.c RSFgen.c RegAna.c
plug_nlfit.c matrix.[ch] Makefile.INCLUDE SUMA/SUMA_MiscFunc.c
- moved matrix.c to libmri.a
30 Jul 2007: nifti updates for regression testing
* modified Makefile, README, Updates.txt
* added Testing/Makefile, and under new Testing/nifti.regress_test directory:
README, @test, @show.diffs, and under new commands directory:
c01.versions, c02.nt.help, c03.hist, c04.disp.anat0.info,
c05.mod.hdr, c06.add.ext, c07.cbl.4bricks, c08.dts.19.36.11,
c09.dts4.compare, c10a.dci.run.210, c10.dci.ts4, c11.add.comment,
c12.check.comments, c13.check.hdrs, c14.make.dsets, c15.new.files
* modified gifti/gtest.c, Makefile: init gfile, add CFLAGS
31 Jul 2007:
* modified 3dAllineate.c, 3dresample.c, 3dSegment.c, 3dSpatNorm.c,
afni_plugin.c, Makefile.INCLUDE, mrilib.h, plug_crender.c,
rickr/3dresample.c, rickr/r_new_resam_dset.c,
SUMA/SUMA_3dSkullStrip.c, whereami.c
- included r_new_resam_dset, r_hex_str_to_long, r_idisp_fd_brick
in forced_loads[]
* modified r_idisp.[ch]: nuked unused r_idisp_cren_stuff
* modified nifti/Makefile, Testing/Makefile, Testing/README_regress, and
renamed to nifti_regress_test, all to remove '.' from dir names
* modified afni_func.c: watch for overflow in jj if ar_fim is garbage
01 Aug 2007:
* modified gifti.[ch], gifti_xml.c, gtest.[ch]
- changed dim0..dim5 to dims[], and nvals to size_t
- added gifti_init_darray_from_attrs and some validation functions
02 Aug 2007: modified file_tool.[ch]: added -disp_hex, -disp_hex{1,2,4}
06 Aug 2007:
* modified Makefile.INCLUDE: added targets libmri.so, libmrix.so
* modified afni_vol2surf.c, afni_func.c: better overflow guards
07 Aug 2007: help update to 3dresample
08 Aug 2007:
* modified RegAna.c: changed the 4 EPSILON values to 10e-12 (from 10e-5),
to allow division by smaller sums of errors, to prevent setting
valid output to zero
* modified nifti1_io.c: for list, valid_nifti_brick_list requires 3 dims
24 Aug 2007:
* removed znzlib/config.h
* incorporated Hans Johnson's changes into nifti tree
27 Aug 2007:
* modified afni_vol2surf.c, for non-big, include ovc[npanes], Mike B reported
31 Aug 2007:
* added model_conv_diffgamma.c, for Rasmus
* modified Makefile.INCLUDE: add model_conv_diffgamma.so to the model list
* modified mri_read_dicom.c: no more AFNI_DICOM_WINDOW warnings
07 Sep 2007:
* modified Makefile.linux_xorg7/_64 to work on Fedora7
* modified model_conv_diffgamma.c: fix diff, never set ts[0] to 1
17 Sep 2007:
* modified 3dDeconvolve.c: show voxel loop when numjobs > 1
* modified model_conv_diffgamma.c: allow no scaling, add more debug
20 Sep 2007: modified thd_opendset.c: THD_deconflict_nifti needs to use path
24 Sep 2007:
* modified 3dbucket.c 3dCM.c 3dnewid.c 3dNotes.c 3drefit.c 3dTcat.c adwarp.c
afni.c plug_notes.c plug_tag.c readme_env.h thd_writedset.c:
- changed AFNI_DONT_DECONFLICT to AFNI_DECONFLICT
- modified default behavior to failure (from deconflict)
* modified 3dTshift.c: help fix for seqplus/seqminus
* modified AFNI.afnirc: set hints to YES as default
27 Sep 2007: modified Makefile.INCLUDE: added @DriveAfni/Suma to SCRIPTS
02 Oct 2007: modified AlphaSim.c: added -seed option
03 Oct 2007:
* modified 3dDeconvolve: use default polort of just 1+floor(rtime/150)
* modified afni_proc.py, db_mod.py: apply same default polort
04 Oct 2007: modified ccalc.c: quit on ctrl-D, no error on empty line
10 Oct 2007:
* modified db_mod.py: need math for floor()
* modified 3dDeconvolve.c: set AFNI_DECONFLICT=OVERWRITE in do_xrestore_stuff
12 Oct 2007: modified thd_niftiread/write.c: get/set nim->toffset
19 Oct 2007: modified mbig.c to handle mallocs above 2 GB
22 Oct 2007:
* modified Makefile.INCLUDE: added R_scripts dir
* checked in Gang's current 3dLME.R and io.R scripts
23 Oct 2007:
* added afni_run_R script, to set AFNI_R_DIR and invoke R
* modified Makefile.INCLUDE, added afni_run_R to SCRIPTS
* modified 3dLME.R, to use the AFNI_R_DIR environment variable
25 Oct 2007: modified 3dfractionize.c: added another help example
26 Oct 2007: gifti 0.2
* renamed gifti.? to gifti_io.?, gtest to gifti_test
* modified get.times, test.io: applied gifti_test name
* modified Makefile: applied name changes, added clean: target
* modified gifti_io.[ch]: prepended 'gifti_' to main data structures
- MetaData -> gifti_MetaData, LabelTable -> gifti_LabelTable,
CoordSystem -> gifti_CoordSystem, DataArray -> gifti_DataArray
* modified gifti_xml.c:
- added indent level to control structure and fixed logic
- allowed more CDATA parents (any PCDATA)
- added ewrite_text_ele and applied ewrite_cdata_ele
* modified gifti_test.c: changed option to -gifti_ver
29 Oct 2007:
* modified gifti*.[ch]: changed gifti datastruct prefixes from gifti_ to gii
* modified test.io: added -nots option, to skip time series
* added README.gifti
30 Oct 2007: sync nifti from sourceforge (from Michael Hanke)
* added LICENSE, Makefile.cross_mingw32, packaging/DevPackage.template
* modified CMakeLists.txt, Updates.txt
08 Nov 2007:
* modified fslio.c: applied Henke fix for FslFileType
* modified nifti_io.c: applied Yaroslav fix for ARM alignment problem
* modified model_demri_3.c: allow for nfirst == 0
09 Nov 2007: modified model_demri_3.c: added AFNI_MODEL_D3_PER_MIN
13 Nov 2007:
* modified adwarp.c: applied AFNI_DECONFLICT for both overwrite and decon
* modified SUMA_Load_Surface_Object.c:
- apply SUMA_SurfaceTypeCode in SUMA_coord_file
14 Nov 2007: modified Makefile.cygwin, Makefile.INCLUDE for cygwin build
* modified adwarp.c: aside from -force, let user's AFNI_DECONFLICT decide
21 Nov 2007: gifti base64 I/O: lib version 0.3
* modified giftio_io.[ch], gifti_xml.[ch], gifti_test.c, test.io
- added I/O routines for base64 via b64_encode_table/b64_decode_table
- append_to_data_b64(), decode_b64(), copy_b64_data
- added b64_check/b64_errors to global struct
- pop_darray: check for b64_errors and byte-swapping
- dind is size_t
- notable functions: gifti_list_index2string, gifti_disp_hex_data
gifti_check_swap, gifti_swap_Nbytes
26 Nov 2007: modified afni_proc.py, db_mod.py: volreg defaults to cubic interp.
28 Nov 2007: nifti updates for GIFTI and datatype_to/from_string
* modified nifti1.h: added 5 new INTENTs for GIFTI, plus RGBA32 types
* modified nifti1.[ch]:
- added NIFTI_ECODE_FREESURFER
- added nifti_type_list, an array of nifti_type_ele structs
* modified nifti_tool.[ch]: added -help_datatypes, to list or test types
* modified nifti_regress_test/commands/c02.nt.help: added -help_datatypes
* modified Updates.txt: for these changes
29 Nov 2007:
* modified nifti1.h, nifti1_io.c: use 2304 for RGBA32 types
* modified gifti_io.c, gifti_xml.c: fixed nvpair value alloc
02 Dec 2007:
* modified Makefile.linux_xorg7: added -D_FILE_OFFSET_BITS=64 for LFS
(will probably do that in other Makefiles)
03 Dec 2007: applied changes for GIFTI Format 1.0 (11/21)
* replaced Category with Intent
* replaced Location attribute with ExternalFileName/Offset
* added NumberOfDataArrays attribute to GIFTI element
* applied new index_order strings
05 Dec 2007: applied changes for NIfTI release 1.0
* modified Updates.txt, Makefile, README, CMakeLists.txt
fsliolib/CMakeLists.txt nifticdf/CMakeLists.txt
niftilib/CMakeLists.txt znzlib/CMakeLists.txt
06 Dec 2007: applied more NIfTI updates: release 1.0.0 (extra 0 :)
* modified Makefile README packaging/nifticlib.spec
08 Dec 2007: allowed ANALYZE headers in nifti_hdr_looks_good
10 Dec 2007: gifticlib 0.6
* modified gifti_io.[ch], gifti_test.[ch], gifti_xml.[ch],
Makefile, README.gifti
- can read/write Base64Binary datasets (can set compress level)
- removed datatype lists (have gifti_type_list)
- added gifti_read_da_list(), with only partial ability
- added GIFTI numDA attribute
- change size_t to long long
* modified 3dresample.c: allowed for AFNI_DECONFLICT
11 Dec 2007: gifticlib 0.7
* modified gifti_io.[ch], gifti_xml.c, gifti_test.c, README.gifti:
- added GIFTI_B64_CHECK defines and disp_gxml_data()
- set b64_check default to SKIPNCOUNT
12 Dec 2007: gifticlib 0.8
* modified gifti_io.[ch], gifti_xml.c:
- added sub-surface selection, via dalist in gifti_read_da_list()
- added gifti_copy_DataArray, and other structures
13 Dec 2007: modified thd_brainnormalize.h: replace unsetenv with putenv(NO)
14 Dec 2007: modified Makefile.linux_gcc33_64 for building on FC3 (was 2)
27 Dec 2007: added Makefile.macosx_10.5_G5, Makefile.macosx_10.5_Intel
- contain -dylib_file option, for resolving 10.5 problem with libGL
28 Dec 2007: gifti_io v0.9 (now, with gifti_tool)
* added gifti_tool.[ch]: replacing gifti_test, with added functionality
* modified gifti_test.[ch]: simplifying the program as a sample
* modified gifti.get.times, gifti.test.io, Makefile: use tifti_tool
* modified gifti_io.[ch], gifti_xml.[ch]:
- made zlib optional, via -DHAVE_ZLIB in compile
(without zlib, the user will get warnings)
- now users only #include gifti_io.h, not gifti_xml, expat or zlib
- added more comments and made tables more readable
- added all user-variable access functions and reset_user_vars()
- added gifti_free_image_contents(), gifti_disp_raw_data(),
gifti_clear_float_zeros() and gifti_set_all_DA_attribs()
- changed gifti_gim_DA_size to long long
- added GIFTI_B64_CHECK_UNDEF as 0
- fixed 0-width indenting and accumulating base64 errors
03 Jan 2008:
* modified gifti_io.[ch], gifti_xml.[ch] (v0.10)
- added top-level gifti_create_image() interface
- must now link libniftiio
- gifti_add_empty_darray() now takes num_to_add
- if data was expected but not read, free it
(can add via gifti_alloc_all_data())
- many minor changes
* modified gifti_tool.[ch] (v0.1)
- can do one of display, write or test (more to come)
- added dset creation ability and options, via -new_dset or MAKE_IM
(options -new_*, for numDA, intent, dtype, ndim, dims, data)
- added AFNI-style DA selection, for input datasets
* modified README.gifti, gifti/Makefile
11 Jan 2008:
* modified mri_to_byte.c afni_vol2surf.c mrilib.h:
- added mri_to_bytemask() and a call to it in afni_vol2surf, for
using the clustered result in vol2surf
* modified gifti_io.[ch], gifti_xml.c, Makefile, README.gifti
- attribute/data setting functions are more flexible
- added gifti_disp_dtd_url, gifti_set_DA_meta, gifti_valid_int_list,
DA_data_exists, gifti_add_to_meta
* modified gifti_tool.[ch]
- added option -gifti_dtd_url
- added options -mod_DAs and -read_DAs (replaced -dalist)
- added options -mod_add_data, -mod_DA_attr, -mod_DA_meta,
-mod_gim_attr, -mod_gim_meta
(modification takes place at dataset read time)
- reformatted help output
16 Jan 2008: giftilib 0.12, gifti_tool 0.3
* modified gifti.test.io: added new -no_updates option
* modified gifti_io.[ch], gifti_xml.[ch], README.gifti:
- added gifti_copy_gifti_image() and gifti_convert_to_float()
- added gifti_valid_LabelTable(), gifticlib_version(),
gifti_copy_LabelTable(), gifti_updaet_nbyper() and
gifti_valid_gifti_image()
- added control over library updates to metadata
- expanded checks in gifti_valid_dims
* modified gifti_tool.[ch]:
- added options -gifti_zlib, -gifti_test, -mod_to_float, -no_updates
* modified gifti/Makefile: in clean_all, rm gifti*.lo*
* modified Makefile.INCLUDE: added gifti_tool target
18 Jan 2008: modified 3dclust.c: fixed "MI RL" description in -help
22 Jan 2008: afni_proc.py updates for estimating smoothness
* modified afni_base.py: added 'short' to comopt.show()
* modified option_list.py: added 'short' to OptionList.show()
* modified afni_proc.py:
- added -show_valid_opts to simply print options
- added -regress_est_blur_epits, -regress_est_blur_errts,
-regress_no_mask and -regress_errts_prefix options
- creation of all_runs always happens now
23 Jan 2008: added useless statements to fix suma crashes on FC7 (compiler?)
* modified SUMA_Load_Surface_Object.c: added optimization appease message
25 Jan 2008: fixed Makefile.linux_gcc32 to linux motif statically
05 Feb 2008: nifti updates for hans johnson to remove nia.gz functionality
* modified cmake_testscripts/newfiles_test.sh, commands/c15.new.files,
utils/nifti1_test.c, niftilib/nifti1_io.c
06 Feb 2008: modified 3dbucket.c to copy fdr curves
13 Feb 2008: beginning GIFTI support in AFNI
* added gifti_choice.c, thd_gifti.c
* modified: 3ddata.h, thd_auxdata.c, thd_info.c, thd_opendset.c,
edt_dsetitems.c, thd_delete.c, thd_loaddblk.c, thd_writedset.c,
thd_fetchdset.c, thd_mastery.c, thd_niml.c, Makefile.INCLUDE
20 Feb 2008: GIFTI to AFNI
* modified 3ddata.h: added dtype_nifti_to_niml prototype
* modified thd_niml.c: added dtype_nifti_to_niml(), plus 2 stupid changes
* modified thd_gifti.c: added functionality to convert GIFTI to NIML/AFNI
* modified gifti_io.[ch]: added gifti_get_meta_value and gifti_image_has_data
* modified Makefile.linux_xorg7_64: to have the option of GIFTI support
21 Feb 2008: GIFTI I/O mostly working
* modified 3ddata.h: added NI_write_gifti(), NI_find_element_by_aname(),
dtype_niml_to_nifti(), nsd_string_atr_to_slist()
* modified gifti_choice.c: changed NI_write_gifti() prototype
* modified thd_niml.c:
- exported nsd_string_atr_to_slist()
- added dtype_niml_to_nifti(), NI_find_element_by_aname()
* modified thd_gifti.c: added functions to convert AFNI->GIFTI
* modified Makefiles: added USE_GIFTI and LGIFTI to uncomment for application
linux_gcc32 linux_gcc33_64 linux_xorg7 macosx_10.4 macosx_10.4_G5
macosx_10.4_Intel macosx_10.5_G5 macosx_10.5_Intel solaris28_gcc
solaris29_suncc solaris29_suncc_64 solaris28_suncc
24 Feb 2008: minor fixes to thd_gifti.c
25 Feb 2008:
* modified gifti_io.c: metadata element without data is valid
* modified afni_vol2surf.c: VEDIT_IVAL against fim_index (not thr_index)
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