- Update to build 2012-04-17 [1]

- Projest has new homepage [1]
- Mark MAKE_JOBS_UNSAFE

PR:		ports/167651 [1]
Submitted by:	Jason Bacon <jwbacon@tds.net> (maintainer) [1]

10 files changed, 691 insertions, 264 deletions

diff --git a/science/afni/Makefile b/science/afni/Makefile
index c00742bfe99c..1d49312999b0 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -15,11 +15,10 @@
 # you can download the latest sources and build manually.
 
 PORTNAME=	afni
-PORTVERSION=	2008.01.02.1043
-PORTREVISION=	6
+PORTVERSION=	2012.04.17.2129
 CATEGORIES=	science biology graphics
-MASTER_SITES=	http://www.neuro.mcw.edu/Ports/distfiles/AFNI/${PORTVERSION}/ \
-		http://afni.nimh.nih.gov/pub/dist/tgz/
+MASTER_SITES=	http://personalpages.tds.net/~jwbacon/Ports/distfiles/AFNI/${PORTVERSION}/ \
+		http://www.acadix.biz/Ports/distfiles/AFNI/${PORTVERSION}/
 DISTFILES=	afni_src.tgz afni.1 3dClustBust.c \
 		TTatlas+tlrc.BRIK.gz TTatlas+tlrc.HEAD CA_EZ_v1.5-July3107.tgz
 DIST_SUBDIR=	AFNI-${PORTVERSION}
@@ -28,6 +27,9 @@ EXTRACT_ONLY=	afni_src.tgz CA_EZ_v1.5-July3107.tgz
 MAINTAINER=	jwbacon@tds.net
 COMMENT=	Advanced Functional Neuro Imaging
 
+LIB_DEPENDS=	Xm:${PORTSDIR}/x11-toolkits/open-motif \
+		R:${PORTSDIR}/math/R \
+		gsl:${PORTSDIR}/math/gsl
 RUN_DEPENDS=	cjpeg:${PORTSDIR}/graphics/jpeg \
 		mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \
 		whirlgif:${PORTSDIR}/graphics/whirlgif \
@@ -46,9 +48,10 @@ USE_GETTEXT=	yes
 USE_GMAKE=	yes
 USE_ICONV=	yes
 USE_MOTIF=	yes
+MAKE_ENV=	CC="${CC}"
+MAKE_JOBS_UNSAFE=yes
 
 WRKSRC=		${WRKDIR}/afni_src
-MAKEFILE=	Makefile.FreeBSD_PORT
 ALL_TARGET=	vastness suma
 
 ###########################################################################
@@ -56,6 +59,8 @@ ALL_TARGET=	vastness suma
 
 MAN1=		afni.1
 
+SUB_FILES=	pkg-message afni.cshrc afni.profile
+
 INSTALL_WRKSRC=	${WRKSRC}/BSD
 STAGE=		${WRKSRC}/stage
 
@@ -68,16 +73,15 @@ X11R6_FILES=	coxplot/Makefile \
 		SUMA/SUMA_Load_Surface_Object.c \
 		SUMA/SUMA_MiscFunc.c \
 		SUMA/SUMA_ParseCommands.c \
-		SUMA/SUMA_StripPath.c \
 		SUMA/GLUT/libglut/glut_event.c \
 		SUMA/SUMA_Surface_IO.c
 
 post-extract:
-	@${CP} -f ${FILESDIR}/Makefile.FreeBSD_PORT ${WRKSRC}
+	@${CP} -f ${FILESDIR}/Makefile.FreeBSD_PORT ${WRKSRC}/Makefile
 .for f in ${X11R6_FILES}
 	@${REINPLACE_CMD} -e 's|/usr/X11R6|$${LOCALBASE}|g' ${WRKSRC}/${f}
 .endfor
-	@${REINPLACE_CMD} -e 's|AFNI_2007_05_29_1644|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h
+	@${REINPLACE_CMD} -E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h
 	@${CP} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${WRKDIR}
 	@${CP} ${DISTDIR}/${DIST_SUBDIR}/3dClustBust.c ${WRKSRC}
 	@${REINPLACE_CMD} "s|%%PREFIX%%|${PREFIX}|g" ${WRKDIR}/afni.1
@@ -95,15 +99,16 @@ post-build:
 	${MV}	${INSTALL_WRKSRC}/*.a \
 		${INSTALL_WRKSRC}/*.so \
 		${STAGE}/lib
-	${MV}	${INSTALL_WRKSRC}/*.jpg \
-		${INSTALL_WRKSRC}/*.txt \
+	${MV}	${INSTALL_WRKSRC}/funstuff \
 		${INSTALL_WRKSRC}/AFNI.*rc \
+		${INSTALL_WRKSRC}/afnigui* \
 		${STAGE}/share
 	${MV}	${INSTALL_WRKSRC}/*.h \
 		${STAGE}/include
 	${MV}	${INSTALL_WRKSRC}/README* \
 		${STAGE}/doc
 	${MV}	${INSTALL_WRKSRC}/abut ${INSTALL_WRKSRC}/afni_abut
+	${MV}	${INSTALL_WRKSRC}/qhull ${INSTALL_WRKSRC}/afni_qhull
 	for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \
 		${MV} $${binary} ${STAGE}/bin ; \
 	done
@@ -114,18 +119,20 @@ do-install:
 	${MKDIR} ${DATADIR} ${PREFIX}/lib/afni ${PREFIX}/include/afni
 	${INSTALL_DATA} ${STAGE}/lib/* ${PREFIX}/lib/afni
 	${INSTALL_DATA} ${STAGE}/include/* ${PREFIX}/include/afni
-	${INSTALL_DATA} ${STAGE}/share/* ${DATADIR}
+	${CP} -R ${STAGE}/share/* ${DATADIR}
 	${INSTALL_PROGRAM} ${STAGE}/bin/* ${PREFIX}/bin
 	${INSTALL_SCRIPT} ${STAGE}/scripts/* ${PREFIX}/bin
 	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/TTatlas* ${DATADIR}
 	${INSTALL_DATA} ${WRKDIR}/CA_EZ_v1.5-July3107/* ${DATADIR}
 	${INSTALL_MAN} ${WRKDIR}/afni.1 ${MAN1PREFIX}/man/man1
 .if !defined(NOPORTDOCS)
-	${MKDIR} ${DOCSDIR}
+	${MKDIR} ${DOCSDIR} ${PREFIX}/etc/mri
 	${INSTALL_DATA} ${STAGE}/doc/* ${DOCSDIR}
+	${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \
+		${PREFIX}/etc/mri
 .endif
 
 post-install:
-	@${CAT} pkg-message
+	@${CAT} ${WRKDIR}/pkg-message
 
 .include <bsd.port.post.mk>
diff --git a/science/afni/distinfo b/science/afni/distinfo
index 6928bdb6c2f1..43783afdeb8c 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -1,12 +1,12 @@
-SHA256 (AFNI-2008.01.02.1043/afni_src.tgz) = 39d190c705ce93e8794500de11c367e0ba0ea6600baac34cdd23cdd2400d18fd
-SIZE (AFNI-2008.01.02.1043/afni_src.tgz) = 12248881
-SHA256 (AFNI-2008.01.02.1043/afni.1) = f134d1f869b1dfd618c61e58fd24b9c4dcfea9c25bc5b1c26dbbb141719cd6f8
-SIZE (AFNI-2008.01.02.1043/afni.1) = 1667
-SHA256 (AFNI-2008.01.02.1043/3dClustBust.c) = 2ca07ff08acc41d7c8895d06ae9effa2c6058aada45fc5381b63a726600dded2
-SIZE (AFNI-2008.01.02.1043/3dClustBust.c) = 106517
-SHA256 (AFNI-2008.01.02.1043/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd
-SIZE (AFNI-2008.01.02.1043/TTatlas+tlrc.BRIK.gz) = 159912
-SHA256 (AFNI-2008.01.02.1043/TTatlas+tlrc.HEAD) = 51c3fb158990616f355fea56886fc7c85d80ac96779f5a65a8f69207c2a85919
-SIZE (AFNI-2008.01.02.1043/TTatlas+tlrc.HEAD) = 1750
-SHA256 (AFNI-2008.01.02.1043/CA_EZ_v1.5-July3107.tgz) = 4300ec3e94b7dfd43f70b3f321f8aa290bd9f6e6420a414f251dbd790df8af02
-SIZE (AFNI-2008.01.02.1043/CA_EZ_v1.5-July3107.tgz) = 2654150
+SHA256 (AFNI-2012.04.17.2129/afni_src.tgz) = 815ff58ef10f2174211e507ac4d527a0025f31e0a54976f5915f8ff3a0a95209
+SIZE (AFNI-2012.04.17.2129/afni_src.tgz) = 18635542
+SHA256 (AFNI-2012.04.17.2129/afni.1) = f134d1f869b1dfd618c61e58fd24b9c4dcfea9c25bc5b1c26dbbb141719cd6f8
+SIZE (AFNI-2012.04.17.2129/afni.1) = 1667
+SHA256 (AFNI-2012.04.17.2129/3dClustBust.c) = 2ca07ff08acc41d7c8895d06ae9effa2c6058aada45fc5381b63a726600dded2
+SIZE (AFNI-2012.04.17.2129/3dClustBust.c) = 106517
+SHA256 (AFNI-2012.04.17.2129/TTatlas+tlrc.BRIK.gz) = 0b5b087006e07e05c5f0c8306acaade955924f744457cec0c00844cc2e9e67cd
+SIZE (AFNI-2012.04.17.2129/TTatlas+tlrc.BRIK.gz) = 159912
+SHA256 (AFNI-2012.04.17.2129/TTatlas+tlrc.HEAD) = 57262785bcc87ef5aa0f0cddc82d67c15e799ac9e2e12127e8eeb4d348ccf55e
+SIZE (AFNI-2012.04.17.2129/TTatlas+tlrc.HEAD) = 1830
+SHA256 (AFNI-2012.04.17.2129/CA_EZ_v1.5-July3107.tgz) = 4300ec3e94b7dfd43f70b3f321f8aa290bd9f6e6420a414f251dbd790df8af02
+SIZE (AFNI-2012.04.17.2129/CA_EZ_v1.5-July3107.tgz) = 2654150
diff --git a/science/afni/files/Makefile.FreeBSD_PORT b/science/afni/files/Makefile.FreeBSD_PORT
index 55f96ce90860..037afd7a3236 100644
--- a/science/afni/files/Makefile.FreeBSD_PORT
+++ b/science/afni/files/Makefile.FreeBSD_PORT
@@ -25,7 +25,7 @@
 #           and under FreeBSD 5.1.
 #
 #   Note:   The SUMA build process (as of Aug, 2003) requires GNU make,
-#           which is /usr/local/bin/gmake on BSD systems.  
+#           which is ${LOCALBASE}/bin/gmake on BSD systems.  
 #           Be sure the MAKE macro below is set to gmake.
 #
 #   Note:   Compilation of netcdf-3.5.0 may fail due to m4's lack of
@@ -61,16 +61,17 @@ CCFAST = ${CC} -O3
 CCMIN  = ${CC}
 CCD    = ${CC} ${CCDEBS}
 CCSVD  = ${CC} -O0
+CCOLD  = ${CC}
 
-IFLAGS = -I. -I${LOCALBASE}/include -I/usr/local/include
-LFLAGS = -s -L. -L${LOCALBASE}/lib
+IFLAGS = -I. -I${X11BASE}/include -I${LOCALBASE}/include
+LFLAGS = -s -L. -L${X11BASE}/lib -L${LOCALBASE}/lib
 
 MAKE   = gmake
 
 PLUGIN_SUFFIX = so
 PLUGIN_LFLAGS = -shared
 PLUGIN_CC     = ${CC}
-PLFLAGS       = -s -rdynamic -L. -L${LOCALBASE}/lib
+PLFLAGS       = -s -rdynamic -L. -L${X11BASE}/lib -L${LOCALBASE}/lib
 
 AR     = /usr/bin/ar
 RANLIB = /usr/bin/ranlib
@@ -90,12 +91,12 @@ LIBDIR = ${INSTALLDIR}
 
 # for dynamic linking
 
-LLIBS  = -lmri -lXm -lXp -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB)
+LLIBS  = -lmri -lf2c -lXm -lXp -lXpm -lXext -lXmu -lXt -lX11 -lm $(LZLIB)
 
 # vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
 # For suma (NO STATIC LINKING OF GL libs)
-SUMA_INCLUDE_PATH = -I${LOCALBASE}/include -I/usr/local/include -I./ -I../ -I../niml/ -Igts/src 
-SUMA_LINK_PATH = -L/usr/lib -L${LOCALBASE}/lib -L../
+SUMA_INCLUDE_PATH = -I${X11BASE}/include -I${LOCALBASE}/include -I./ -I../ -I../niml/ -Igts/src 
+SUMA_LINK_PATH = -L/usr/lib -L${X11BASE}/lib -L${LOCALBASE}/lib -L../
 #use -lGLw if you have libGLw.a or libGLw.so* or 
 #  -lMesaGLw if you have Mesa's version (libMesaGLw*) of libGLw
 SUMA_LINK_LIB = -lXm -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext -lX11 -lm $(LZLIB)
diff --git a/science/afni/files/afni.cshrc.in b/science/afni/files/afni.cshrc.in
new file mode 100644
index 000000000000..4b0ddfd1c881
--- /dev/null
+++ b/science/afni/files/afni.cshrc.in
@@ -0,0 +1,2 @@
+setenv AFNI_PLUGINPATH %%PREFIX%%/lib/afni:%%DATADIR%%
+setenv AFNI_GLOBAL_SESSION %%DATADIR%%
diff --git a/science/afni/files/afni.profile.in b/science/afni/files/afni.profile.in
new file mode 100644
index 000000000000..0bddb1129f53
--- /dev/null
+++ b/science/afni/files/afni.profile.in
@@ -0,0 +1,4 @@
+AFNI_PLUGINPATH=%%PREFIX%%/lib/afni:%%DATADIR%%
+export AFNI_PLUGINPATH
+AFNI_GLOBAL_SESSION=%%DATADIR%%
+export AFNI_GLOBAL_SESSION
diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE
index 718c70ede6eb..589f7546e7ca 100644
--- a/science/afni/files/patch-Makefile.INCLUDE
+++ b/science/afni/files/patch-Makefile.INCLUDE
@@ -1,21 +1,21 @@
---- Makefile.INCLUDE.orig	Thu Jun  7 13:40:04 2007
-+++ Makefile.INCLUDE	Thu Aug 30 14:12:08 2007
-@@ -41,7 +41,7 @@
+--- Makefile.INCLUDE.orig	2012-04-17 15:56:21.000000000 -0500
++++ Makefile.INCLUDE	2012-04-18 13:39:29.000000000 -0500
+@@ -48,7 +48,7 @@
  ## AFNI package, but included because they are useful.  Some of
  ## them are Open Source programs, not from the AFNI group at all.
  
--EXTRAS   = cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv $(EXPROGS)
+-EXTRAS   = cjpeg djpeg whirlgif mpeg_encode myget Xphace rmz aiv mycat $(EXPROGS)
 +EXTRAS   = myget Xphace rmz aiv 3dClustBust $(EXPROGS)
  
  # mpegtoppm in above list
  
-@@ -234,6 +234,9 @@
- 
+@@ -282,6 +282,9 @@
  3dbuc2fim:3dbuc2fim.o
  	$(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)
-+
+ 
 +3dClustBust:3dClustBust.c
 +	$(CC) -o 3dClustBust 3dClustBust.c $(INFLAGS) $(LFLAGS) $(LLIBS)
- 
++
  mritopgm:mritopgm.c
  	$(CC) -o mritopgm mritopgm.c $(INFLAGS) $(LFLAGS) $(LLIBS)
+ 
diff --git a/science/afni/files/patch-misc_math.c b/science/afni/files/patch-misc_math.c
new file mode 100644
index 000000000000..08b62b57fe95
--- /dev/null
+++ b/science/afni/files/patch-misc_math.c
@@ -0,0 +1,16 @@
+--- misc_math.c.orig	2012-04-18 13:42:55.000000000 -0500
++++ misc_math.c	2012-04-18 13:43:41.000000000 -0500
+@@ -1,6 +1,13 @@
+ 
++/* For older libm */
++double log2(double n)
++{
++    return log(n) / log(2.0);
++}
++
+ /* move from Deconvolve.c into libmri.a         21 Jun 2010 [rickr] */
+ 
++
+ double legendre( double x , int m )   /* Legendre polynomials over [-1,1] */
+ {
+    if( m < 0 ) return 1.0 ;    /* bad input */
diff --git a/science/afni/pkg-message b/science/afni/files/pkg-message.in
index 6e2108a4534a..04b0f86e4681 100644
--- a/science/afni/pkg-message
+++ b/science/afni/files/pkg-message.in
@@ -1,22 +1,28 @@
 =============================================================================
-Run "man afni" for information on setting up your afni environment.
-
-For questions or comments regarding the FreeBSD port, please contact the
-port maintainer: 
-
-jwbacon@tds.net
+For quick info, run "man afni".
 
 For AFNI configuration and usage, please visit the AFNI WEB site at 
 
 http://afni.nimh.nih.gov.
 
-SUMA requires the nvidia graphics driver or DRI.
+---
+
+SUMA requires the nVidia graphics driver (x11/nvidia-driver*)
+or DRI (graphics/dri).
+
+---
 
 For large 3dDeconvolve analyses, you may need to increase the shared
-memory limit on your system.  For instructions, visit
+memory limit on your system.
 
-http://www.neuro.mcw.edu/~bacon/Ports/FreeBSD/shared_mem.html
+---
 
 The program "abut" has been renamed "afni_abut" to resolve a collision
 with the unixstat port.
+
+---
+
+AFNI_PLUGIN_PATH should be set to %%PREFIX%%/lib/afni:%%DATADIR%%
+AFNI_GLOBAL_SESSION should be set to %%DATADIR%%.
+
 =============================================================================
diff --git a/science/afni/pkg-descr b/science/afni/pkg-descr
index 599ff178f36c..a4cd1efaa5c7 100644
--- a/science/afni/pkg-descr
+++ b/science/afni/pkg-descr
@@ -2,4 +2,4 @@ This is a port of AFNI, Analysis of Functional Neuro Imaging.  AFNI is
 a tool for analyzing 3 dimensional images, especially functional MRI
 images used in brain mapping research.
 
-WWW: http://www.neuro.mcw.edu/Ports
+WWW:	http://afni.nimh.nih.gov/afni/
diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index ad1087e6e54a..b104f83a875f 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -1,10 +1,23 @@
+bin/1dAstrip
+bin/1dBandpass
+bin/1dBport
+bin/1dCorrelate
 bin/1dFlagMotion
+bin/1dGC.R
 bin/1dMarry
+bin/1dRplot
+bin/1dRplot.R
 bin/1dSEM
+bin/1dSEMr.R
+bin/1dSVAR.R
+bin/1dTsort
+bin/1dUpsample
+bin/1d_tool.py
 bin/1dcat
 bin/1ddot
 bin/1deval
 bin/1dfft
+bin/1dgenARMA11
 bin/1dgrayplot
 bin/1dmatcalc
 bin/1dnorm
@@ -15,6 +28,7 @@ bin/1dtranspose
 bin/24swap
 bin/2dImReg
 bin/2swap
+bin/3dABoverlap
 bin/3dAFNIto3D
 bin/3dAFNItoANALYZE
 bin/3dAFNItoMINC
@@ -34,15 +48,20 @@ bin/3dAutoTcorrelate
 bin/3dAutobox
 bin/3dAutomask
 bin/3dBRAIN_VOYAGERtoAFNI
+bin/3dBandpass
+bin/3dBlurInMask
 bin/3dBlurToFWHM
 bin/3dBrickStat
 bin/3dCM
 bin/3dCRUISEtoAFNI
 bin/3dClipLevel
 bin/3dClustBust
+bin/3dClustSim
 bin/3dConvolve
+bin/3dCountSpikes
 bin/3dDFT
 bin/3dDTeig
+bin/3dDTtoDWI
 bin/3dDWItoDT
 bin/3dDeconvolve
 bin/3dDeconvolve_f
@@ -50,32 +69,59 @@ bin/3dDespike
 bin/3dDetrend
 bin/3dEmpty
 bin/3dEntropy
+bin/3dErrtsCormat
 bin/3dExtrema
 bin/3dFDR
+bin/3dFFT
 bin/3dFWHM
 bin/3dFWHMx
 bin/3dFourier
 bin/3dFriedman
+bin/3dGC.R
+bin/3dGenPriors
 bin/3dGetrow
+bin/3dGroupInCorr
+bin/3dICA.R
+bin/3dICC.R
+bin/3dICC_REML.R
 bin/3dIntracranial
 bin/3dInvFMRI
+bin/3dKS.R
 bin/3dKruskalWallis
 bin/3dLME.R
 bin/3dLRflip
+bin/3dLSS
 bin/3dLocalBistat
+bin/3dLocalPV
+bin/3dLocalSVD
 bin/3dLocalstat
+bin/3dMEMA
+bin/3dMEMA.R
 bin/3dMINCtoAFNI
 bin/3dMannWhitney
+bin/3dMaskToASCII
 bin/3dMax
 bin/3dMean
 bin/3dMedianFilter
 bin/3dNLfim
+bin/3dNormalityTest
 bin/3dNotes
+bin/3dNwarpApply
+bin/3dNwarpCalc
 bin/3dOverlap
 bin/3dPAR2AFNI.pl
+bin/3dPeriodogram
+bin/3dPolyfit
+bin/3dREMLfit
 bin/3dROIstats
+bin/3dRank
 bin/3dRegAna
+bin/3dRetinoPhase
 bin/3dRowFillin
+bin/3dSeg
+bin/3dSetupGroupInCorr
+bin/3dSignatures
+bin/3dSignatures.R
 bin/3dSkullStrip
 bin/3dSpatNorm
 bin/3dStatClust
@@ -85,8 +131,12 @@ bin/3dSynthesize
 bin/3dTSgen
 bin/3dTagalign
 bin/3dTcat
+bin/3dTcorr1D
+bin/3dTcorrMap
 bin/3dTcorrelate
+bin/3dTfitter
 bin/3dThreetoRGB
+bin/3dTnorm
 bin/3dToutcount
 bin/3dTqual
 bin/3dTshift
@@ -96,12 +146,14 @@ bin/3dTstat
 bin/3dTwotoComplex
 bin/3dUndump
 bin/3dUniformize
+bin/3dUpsample
 bin/3dVol2Surf
 bin/3dWarp
 bin/3dWarpDrive
 bin/3dWavelets
 bin/3dWilcoxon
 bin/3dWinsor
+bin/3dXYZcat
 bin/3dZcat
 bin/3dZcutup
 bin/3dZeropad
@@ -121,10 +173,14 @@ bin/3dfim
 bin/3dfim+
 bin/3dfractionize
 bin/3dhistog
+bin/3dinfill
 bin/3dinfo
+bin/3dkmeans
+bin/3dmaskSVD
 bin/3dmaskave
 bin/3dmaskdump
 bin/3dmatcalc
+bin/3dmatmult
 bin/3dmaxima
 bin/3dmerge
 bin/3dnewid
@@ -139,51 +195,97 @@ bin/3dretroicor
 bin/3drotate
 bin/3dsvm
 bin/3dttest
+bin/3dttest++
 bin/3dvolreg
 bin/4swap
+bin/@1dDiffMag
 bin/@2dwarper
+bin/@2dwarper.Allin
 bin/@4Daverage
+bin/@ANATICOR
+bin/@AddEdge
+bin/@AfniEnv
 bin/@AfniOrient2RAImap
 bin/@AfniOrientSign
 bin/@Align_Centers
+bin/@Atlasize
 bin/@Center_Distance
 bin/@CheckForAfniDset
 bin/@CommandGlobb
+bin/@DO.examples
 bin/@DTI_studio_reposition
+bin/@DeblankFileNames
+bin/@DiceMetric
 bin/@DoPerRoi.py
 bin/@DriveAfni
 bin/@DriveSuma
+bin/@ElectroGrid
+bin/@FS_roi_label
+bin/@FSlabel2dset
 bin/@FindAfniDsetPath
 bin/@FromRAI
+bin/@FullPath
+bin/@GetAfniBin
+bin/@GetAfniDims
 bin/@GetAfniID
 bin/@GetAfniOrient
 bin/@GetAfniPrefix
+bin/@GetAfniRes
 bin/@GetAfniView
+bin/@Install_InstaCorr_Demo
 bin/@IsoMasks
+bin/@MakeLabelTable
 bin/@NoExt
+bin/@NoPound
+bin/@NoisySkullStrip
 bin/@Purify_1D
+bin/@Quiet_Talkers
+bin/@ROI_Corr_Mat
+bin/@R_funclist
 bin/@RenamePanga
+bin/@Reorder
+bin/@RetinoProc
 bin/@SUMA_AlignToExperiment
 bin/@SUMA_FSvolToBRIK
 bin/@SUMA_Make_Spec_Caret
 bin/@SUMA_Make_Spec_FS
 bin/@SUMA_Make_Spec_SF
+bin/@ScaleVolume
+bin/@ScriptCheck
+bin/@Shift_Volume
+bin/@ShowDynamicRange
+bin/@Spharm.examples
 bin/@SurfSmooth.HEAT_07.examples
+bin/@TimeDiff
 bin/@ToRAI
 bin/@UpdateAfni
 bin/@VolCenter
 bin/@align_partial_oblique
 bin/@auto_align
 bin/@auto_tlrc
+bin/@build_afni_Xlib
+bin/@clean_help_dir
 bin/@clip_volume
+bin/@demo_prompt
 bin/@escape-
+bin/@fast_roi
 bin/@fix_FSsphere
 bin/@float_fix
+bin/@global_parse
+bin/@help.AFNI
 bin/@isOblique
+bin/@make_plug_diff
 bin/@make_stim_file
 bin/@np
 bin/@parse_afni_name
 bin/@parse_name
+bin/@radial_correlate
+bin/@statauxcode
+bin/@update.afni.binaries
+bin/AFNI_Batch_R
+bin/AFNI_atlas_spaces.niml
+bin/AFNIio.R
+bin/AFNIplot.R
 bin/AlphaSim
 bin/AnalyzeTrace
 bin/CompareSurfaces
@@ -194,13 +296,16 @@ bin/CreateIcosahedron
 bin/DTIStudioFibertoSegments
 bin/Dimon
 bin/DriveSuma
+bin/ExamineXmat
+bin/ExamineXmat.R
 bin/FD2
 bin/FSread_annot
 bin/Ifile
-bin/Imon
 bin/IsoSurface
+bin/Level2.R
 bin/MakeColorMap
 bin/MapIcosahedron
+bin/ParseName
 bin/ROI2dataset
 bin/ROIgrow
 bin/RSFgen
@@ -209,13 +314,20 @@ bin/SUMA_paperplane
 bin/SUMA_pixmap2eps
 bin/SampBias
 bin/ScaleToMap
+bin/Signatures.R
+bin/SpharmDeco
+bin/SpharmReco
 bin/Surf2VolCoord
 bin/SurfClust
+bin/SurfDist
 bin/SurfDsetInfo
+bin/SurfExtrema
+bin/SurfFWHM
 bin/SurfInfo
 bin/SurfMeasures
 bin/SurfPatch
 bin/SurfQual
+bin/SurfRetinoMap
 bin/SurfSmooth
 bin/SurfToSurf
 bin/SurfaceMetrics
@@ -225,11 +337,16 @@ bin/adwarp
 bin/afni
 bin/afni_abut
 bin/afni_base.py
+bin/afni_history
 bin/afni_proc.py
+bin/afni_qhull
 bin/afni_run_R
 bin/afni_util.py
 bin/afni_vcheck
+bin/afni_xmat.py
 bin/aiv
+bin/align_epi_anat.py
+bin/apsearch
 bin/ask_me.py
 bin/byteorder
 bin/cat_matvec
@@ -237,9 +354,14 @@ bin/ccalc
 bin/cdf
 bin/count
 bin/db_mod.py
+bin/demo.fixed.niml.do
+bin/demo.mobile.niml.do
 bin/dicom_hdr
+bin/dicom_hinfo
 bin/dicom_to_raw
+bin/eg_main_chrono.py
 bin/ent16
+bin/fdrval
 bin/fftest
 bin/file_tool
 bin/fim2
@@ -247,6 +369,14 @@ bin/float_scan
 bin/from3d
 bin/ftosh
 bin/ge_header
+bin/gen_epi_review.py
+bin/gen_group_command.py
+bin/gen_ss_review_scripts.py
+bin/gui_uber_align_test.py
+bin/gui_uber_skel.py
+bin/gui_uber_subj.py
+bin/gui_uber_ttest.py
+bin/gui_xmat.py
 bin/im2niml
 bin/imand
 bin/imaver
@@ -261,53 +391,102 @@ bin/imstack
 bin/imstat
 bin/imupsam
 bin/inspec
-bin/io.R
+bin/lib_RR_plot.py
+bin/lib_afni1D.py
+bin/lib_matplot.py
+bin/lib_qt_gui.py
+bin/lib_realtime.py
+bin/lib_subjects.py
+bin/lib_surf_clustsim.py
+bin/lib_textdata.py
+bin/lib_timing.py
+bin/lib_uber_align.py
+bin/lib_uber_skel.py
+bin/lib_uber_subject.py
+bin/lib_uber_ttest.py
+bin/lib_wx.py
+bin/lpc_align.py
+bin/make_pq_script.py
+bin/make_random_timing.py
 bin/make_stim_times.py
 bin/mayo_analyze
+bin/module_test_lib.py
 bin/mritopgm
 bin/myget
+bin/neuro_deconvolve.py
 bin/nicat
+bin/niccc
 bin/nifti1_test
 bin/nifti_tool
+bin/niml_feedme
 bin/nsize
 bin/option_list.py
-bin/p2t
 bin/plugout_drive
 bin/plugout_ijk
 bin/plugout_tt
 bin/plugout_tta
-bin/qhull
+bin/prompt_user
+bin/python_module_test.py
+bin/qdelaunay
+bin/quick.alpha.vals.py
 bin/quickspec
+bin/rbox
+bin/realtime_receiver.py
 bin/rmz
 bin/rotcom
 bin/rtfeedme
 bin/serial_helper
 bin/sfim
 bin/siemens_vision
+bin/slow_surf_clustsim.py
+bin/smooth.R
 bin/sqwave
 bin/strblast
 bin/suma
 bin/suma_change_spec
 bin/tfim
+bin/timing_tool.py
 bin/to3d
+bin/uber_align_test.py
+bin/uber_proc.py
+bin/uber_skel.py
+bin/uber_subject.py
+bin/uber_ttest.py
+bin/ui_xmat.py
 bin/waver
 bin/whereami
+bin/xmat_tool.py
+etc/mri/afni.cshrc
+etc/mri/afni.profile
 include/afni/3ddata.h
+include/afni/AFNI_label.h
+include/afni/Amalloc.h
 include/afni/afni_environ.h
+include/afni/afni_suma.h
 include/afni/afni_warp.h
 include/afni/coxplot.h
 include/afni/cs.h
 include/afni/cs_sort_template.h
+include/afni/debugtrace.h
 include/afni/editvol.h
 include/afni/eispack.h
 include/afni/f2c.h
 include/afni/killer.h
+include/afni/list_struct.h
 include/afni/machdep.h
 include/afni/mcw_glob.h
 include/afni/mcw_malloc.h
+include/afni/mri_dicom_stuff.h
+include/afni/mri_warpfield.h
 include/afni/mrilib.h
 include/afni/multivector.h
+include/afni/nifti1.h
+include/afni/nifti1_io.h
+include/afni/nifticdf.h
 include/afni/niml.h
+include/afni/r_idisp.h
+include/afni/r_misc.h
+include/afni/r_new_resam_dset.h
 include/afni/tagset.h
 include/afni/thd_compress.h
 include/afni/thd_iochan.h
@@ -315,6 +494,9 @@ include/afni/thd_maker.h
 include/afni/vecmat.h
 include/afni/vol2surf.h
 include/afni/volpack.h
+include/afni/znzlib.h
+lib/afni/R_io.so
+lib/afni/libGLws.a
 lib/afni/libSUMA.a
 lib/afni/libcoxplot.a
 lib/afni/libmri.a
@@ -328,6 +510,10 @@ lib/afni/model_convgamma2a.so
 lib/afni/model_demri_3.so
 lib/afni/model_diffexp.so
 lib/afni/model_diffusion.so
+lib/afni/model_exp.so
+lib/afni/model_expMEMRI.so
+lib/afni/model_expMEMRI3.so
+lib/afni/model_expr2.so
 lib/afni/model_gammavar.so
 lib/afni/model_linear.so
 lib/afni/model_linplusort.so
@@ -347,6 +533,8 @@ lib/afni/plug_3ddup.so
 lib/afni/plug_3dsvm.so
 lib/afni/plug_4Ddump.so
 lib/afni/plug_L1fit.so
+lib/afni/plug_afnihistory.so
+lib/afni/plug_aslA3D3.so
 lib/afni/plug_betafit.so
 lib/afni/plug_clust.so
 lib/afni/plug_compress.so
@@ -407,217 +595,418 @@ lib/afni/plug_zeropad.so
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