Date: Sun, 6 May 2012 19:38:35 GMT From: Jason Bacon <jwbacon@tds.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/167651: maintainer update: science/afni Message-ID: <201205061938.q46JcZi3014228@red.freebsd.org> Resent-Message-ID: <201205061940.q46Je0Jt057185@freefall.freebsd.org>
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>Number: 167651 >Category: ports >Synopsis: maintainer update: science/afni >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Sun May 06 19:40:00 UTC 2012 >Closed-Date: >Last-Modified: >Originator: Jason Bacon >Release: 9.0-RELEASE >Organization: Acadix Consulting, LLC >Environment: FreeBSD sculpin.jbacon.dyndns.org 9.0-RELEASE FreeBSD 9.0-RELEASE #0: Tue Jan 3 07:46:30 UTC 2012 root@farrell.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC amd64 >Description: 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://afni.nimh.nih.gov/afni/ Update to build 2012-04-17. >How-To-Repeat: >Fix: Patch attached with submission follows: ===> Generating patch ===> Viewing diff with more diff -ruN --exclude=CVS /usr/ports/science/afni/Makefile /home/bacon/Prog/Ports/ports/science/afni/Makefile --- /usr/ports/science/afni/Makefile 2011-05-02 07:44:49.000000000 -0500 +++ /home/bacon/Prog/Ports/ports/science/afni/Makefile 2012-05-06 13:59:22.000000000 -0500 @@ -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 +27,8 @@ MAINTAINER= jwbacon@tds.net COMMENT= Advanced Functional Neuro Imaging +LIB_DEPENDS= Xm:${PORTSDIR}/x11-toolkits/open-motif \ + R:${PORTSDIR}/math/R RUN_DEPENDS= cjpeg:${PORTSDIR}/graphics/jpeg \ mpeg_encode:${PORTSDIR}/multimedia/mpeg_encode \ whirlgif:${PORTSDIR}/graphics/whirlgif \ @@ -46,9 +47,9 @@ USE_GMAKE= yes USE_ICONV= yes USE_MOTIF= yes +MAKE_ENV= CC="${CC}" WRKSRC= ${WRKDIR}/afni_src -MAKEFILE= Makefile.FreeBSD_PORT ALL_TARGET= vastness suma ########################################################################### @@ -56,6 +57,8 @@ MAN1= afni.1 +SUB_FILES= pkg-message afni.cshrc afni.profile + INSTALL_WRKSRC= ${WRKSRC}/BSD STAGE= ${WRKSRC}/stage @@ -68,16 +71,15 @@ SUMA/SUMA_Load_Surface_Object.c \ SUMA/SUMA_MiscFunc.c \ SUMA/SUMA_ParseCommands.c \ - SUMA/SUMA_StripPath.c \ SUMA/GLUT/libglut/glut_event.c \ SUMA/SUMA_Surface_IO.c post-extract: - @${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|$${LOCALBASE}|g' ${WRKSRC}/${f} .endfor - @${REINPLACE_CMD} -e 's|AFNI_2007_05_29_1644|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h + @${REINPLACE_CMD} -E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h @${CP} ${DISTDIR}/${DIST_SUBDIR}/afni.1 ${WRKDIR} @${CP} ${DISTDIR}/${DIST_SUBDIR}/3dClustBust.c ${WRKSRC} @${REINPLACE_CMD} "s|%%PREFIX%%|${PREFIX}|g" ${WRKDIR}/afni.1 @@ -95,15 +97,16 @@ ${MV} ${INSTALL_WRKSRC}/*.a \ ${INSTALL_WRKSRC}/*.so \ ${STAGE}/lib - ${MV} ${INSTALL_WRKSRC}/*.jpg \ - ${INSTALL_WRKSRC}/*.txt \ + ${MV} ${INSTALL_WRKSRC}/funstuff \ ${INSTALL_WRKSRC}/AFNI.*rc \ + ${INSTALL_WRKSRC}/afnigui* \ ${STAGE}/share ${MV} ${INSTALL_WRKSRC}/*.h \ ${STAGE}/include ${MV} ${INSTALL_WRKSRC}/README* \ ${STAGE}/doc ${MV} ${INSTALL_WRKSRC}/abut ${INSTALL_WRKSRC}/afni_abut + ${MV} ${INSTALL_WRKSRC}/qhull ${INSTALL_WRKSRC}/afni_qhull for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \ ${MV} $${binary} ${STAGE}/bin ; \ done @@ -114,18 +117,20 @@ ${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 -ruN --exclude=CVS /usr/ports/science/afni/distinfo /home/bacon/Prog/Ports/ports/science/afni/distinfo --- /usr/ports/science/afni/distinfo 2011-07-03 08:22:11.000000000 -0500 +++ /home/bacon/Prog/Ports/ports/science/afni/distinfo 2012-05-06 14:08:17.000000000 -0500 @@ -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 -ruN --exclude=CVS /usr/ports/science/afni/files/Makefile.FreeBSD_PORT /home/bacon/Prog/Ports/ports/science/afni/files/Makefile.FreeBSD_PORT --- /usr/ports/science/afni/files/Makefile.FreeBSD_PORT 2008-04-19 12:53:16.000000000 -0500 +++ /home/bacon/Prog/Ports/ports/science/afni/files/Makefile.FreeBSD_PORT 2012-04-18 12:49:11.000000000 -0500 @@ -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 @@ 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 @@ # 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 -ruN --exclude=CVS /usr/ports/science/afni/files/afni.cshrc.in /home/bacon/Prog/Ports/ports/science/afni/files/afni.cshrc.in --- /usr/ports/science/afni/files/afni.cshrc.in 1969-12-31 18:00:00.000000000 -0600 +++ /home/bacon/Prog/Ports/ports/science/afni/files/afni.cshrc.in 2008-01-30 14:26:33.000000000 -0600 @@ -0,0 +1,2 @@ +setenv AFNI_PLUGINPATH %%PREFIX%%/lib/afni:%%DATADIR%% +setenv AFNI_GLOBAL_SESSION %%DATADIR%% diff -ruN --exclude=CVS /usr/ports/science/afni/files/afni.profile.in /home/bacon/Prog/Ports/ports/science/afni/files/afni.profile.in --- /usr/ports/science/afni/files/afni.profile.in 1969-12-31 18:00:00.000000000 -0600 +++ /home/bacon/Prog/Ports/ports/science/afni/files/afni.profile.in 2008-01-30 14:27:02.000000000 -0600 @@ -0,0 +1,4 @@ +AFNI_PLUGINPATH=%%PREFIX%%/lib/afni:%%DATADIR%% +export AFNI_PLUGINPATH +AFNI_GLOBAL_SESSION=%%DATADIR%% +export AFNI_GLOBAL_SESSION diff -ruN --exclude=CVS /usr/ports/science/afni/files/patch-Makefile.INCLUDE /home/bacon/Prog/Ports/ports/science/afni/files/patch-Makefile.INCLUDE --- /usr/ports/science/afni/files/patch-Makefile.INCLUDE 2008-01-28 10:42:02.000000000 -0600 +++ /home/bacon/Prog/Ports/ports/science/afni/files/patch-Makefile.INCLUDE 2012-04-18 13:43:43.000000000 -0500 @@ -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 -ruN --exclude=CVS /usr/ports/science/afni/files/patch-misc_math.c /home/bacon/Prog/Ports/ports/science/afni/files/patch-misc_math.c --- /usr/ports/science/afni/files/patch-misc_math.c 1969-12-31 18:00:00.000000000 -0600 +++ /home/bacon/Prog/Ports/ports/science/afni/files/patch-misc_math.c 2012-04-18 13:43:43.000000000 -0500 @@ -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 -ruN --exclude=CVS /usr/ports/science/afni/files/pkg-message.in /home/bacon/Prog/Ports/ports/science/afni/files/pkg-message.in --- /usr/ports/science/afni/files/pkg-message.in 1969-12-31 18:00:00.000000000 -0600 +++ /home/bacon/Prog/Ports/ports/science/afni/files/pkg-message.in 2012-04-18 11:36:29.000000000 -0500 @@ -0,0 +1,28 @@ +============================================================================= +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 (x11/nvidia-driver*) +or DRI (graphics/dri). + +--- + +For large 3dDeconvolve analyses, you may need to increase the shared +memory limit on your system. + +--- + +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 -ruN --exclude=CVS /usr/ports/science/afni/pkg-descr /home/bacon/Prog/Ports/ports/science/afni/pkg-descr --- /usr/ports/science/afni/pkg-descr 2011-10-24 04:10:44.000000000 -0500 +++ /home/bacon/Prog/Ports/ports/science/afni/pkg-descr 2012-05-06 14:36:52.000000000 -0500 @@ -2,4 +2,4 @@ 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 -ruN --exclude=CVS /usr/ports/science/afni/pkg-message /home/bacon/Prog/Ports/ports/science/afni/pkg-message --- /usr/ports/science/afni/pkg-message 2009-06-19 15:06:30.000000000 -0500 +++ /home/bacon/Prog/Ports/ports/science/afni/pkg-message 1969-12-31 18:00:00.000000000 -0600 @@ -1,22 +0,0 @@ -============================================================================= -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 AFNI configuration and usage, please visit the AFNI WEB site at - -http://afni.nimh.nih.gov. - -SUMA requires the nvidia graphics driver or DRI. - -For large 3dDeconvolve analyses, you may need to increase the shared -memory limit on your system. For instructions, visit - -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. -============================================================================= diff -ruN --exclude=CVS /usr/ports/science/afni/pkg-plist /home/bacon/Prog/Ports/ports/science/afni/pkg-plist --- /usr/ports/science/afni/pkg-plist 2008-01-28 10:42:01.000000000 -0600 +++ /home/bacon/Prog/Ports/ports/science/afni/pkg-plist 2012-05-06 13:32:46.000000000 -0500 @@ -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/24swap bin/2dImReg bin/2swap +bin/3dABoverlap bin/3dAFNIto3D bin/3dAFNItoANALYZE bin/3dAFNItoMINC @@ -34,15 +48,20 @@ 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/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/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/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/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/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/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_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/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/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/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/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/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_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_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 @@ %%DATADIR%%/TT_N27_EZ_ML+tlrc.HEAD %%DATADIR%%/TTatlas+tlrc.BRIK.gz %%DATADIR%%/TTatlas+tlrc.HEAD 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