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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