CompilingCompiling
Step 3: Get and setup AFNI
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export BASE_DIR=/nfsscratch/PREDICT/hjohnson/20121205_src/mkdir -p ${BASE_DIR} cd ${BASE_DIR}curl http://afni.nimh.nih.gov/pub/dist/tgz/afni_src.tgz -o afni_src.tgztar xfz afni_src.tgz# Optional: rm /nfsscratch/PREDICT/hjohnson/20121121_src/afni_src.tgz## NOTE: Suma won't build SUMA because of missing GL library, and wont build parallel because it is stupidcd afni_srcls Makefile*sed 's#/usr/bin/gcc#/usr/bin/gcc44#g' Makefile.linux_gcc33_64 | \sed 's#/usr/X11R6/include#/usr/include#g' | \sed 's#/usr/X11R6/lib64#/usr/lib64#g' | \sed 's#LLIBS *= \(.*\)#LLIBS = \1 -lpng -ljpeg -lXm#g' | \sed 's%^ *INSTALL_PREREQ%#%g' |sed 's%INSTALLDIR = ./linux_gcc33_64%INSTALLDIR = ./linux_RHEL5%g' > Makefile make -j1 totality |
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Step 1: Get and install f2c
cd /nfsscratch/PREDICT/hjohnson/20121121_src/# Install f2c executablersync -avz netlib.org::netlib/f2c/src f2ccd f2cmkdir -p bin share/man/man1cd src make -f makefile.ucp f2c ../bincp f2c.1t ../share/man/man1 # Install f2c librarycd .. # PWD == /nfsscratch/PREDICT/hjohnson/20121121_src/f2ccurl http://www.netlib.org/f2c/libf2c.zip>libf2c.zipmkdir libf2c libcd libf2cunzip ../libf2c.zipmake -f makefile.umake -f makefile.u install LIBDIR=../lib # Create the module file for f2cecho -e "#%Module\n\proc ModuleHelp { } {\n\ puts stderr " This module loads the Fortran-to-C" \n\ puts stderr " compiler f2c into your local environment."\n\ puts stderr " Creation date: 2012-12-05"\n\}\n\set env_base /nfsscratch/PREDICT/hjohnson/20121121_src/f2c\n\module-whatis "module for Fortran-to-C compiler f2c "\n\set curMod [module-info name]\n\prepend-path PATH $env_base/bin\n\prepend-path LD_LIBRARY_PATH $env_base/lib\n\prepend-path MANPATH $env_base/share/man" > ~/privatemodules/f2c |
Step 2: Get and install X11
# Possible solution:sudo yum --installroot=/nfsscratch/PREDICT/hjohnson/20121121_src/X11 install xorg-x11-drivers.x86_64####################### IGNORE #################################cd /nfsscratch/PREDICT/hjohnson/20121121_src/mkdir X11cd X11wget -A tar.gz -r http://www.x.org/releases/X11R7.7/src/mv www.x.org/releases/X11R7.7 ./rm -rf www.x.orgcd X11R7.7/protofor FILE in `ls`; do tar xvf $FILE; done tar xvf libX11-1.5.0.tar.gzcd libX11-1.5.0 # Create the module file for X11R7.7mkdir ~/privatemodules/X11echo -e "#%Module\n\proc ModuleHelp { } {\n\ puts stderr " This module loads X11" \n\ puts stderr " into your local environment."\n\ puts stderr " Creation date: 2012-12-05"\n\}\n\set env_base /nfsscratch/PREDICT/hjohnson/20121121_src/X11\n\module-whatis "module for full X11 "\n\set curMod [module-info name]\n\setenv X11_DEFAULT R7.7prepend-path PATH $env_base/bin\n\prepend-path LD_LIBRARY_PATH $env_base/lib\n\prepend-path MANPATH $env_base/share/man" > ~/privatemodules/X11/R7.7 # Specify the module version for X11echo -e "#%Module\n\\n\if [info exists env(X11_DEFAULT)] {\n\ set ModulesVersion $env(X11_DEFAULT)\n\} else {\n\ set ModulesVersion "R7.7"\n\}" > ~/privatemodules/X11/.version####################### IGNORE ################################# |
# Edit Makefile to use /usr/bin/gcc44 and not X11
Makefile (edited)
# This Makefile works on Linux.# This is for compiling with GCC 4.4, on a 64-bit CPU.GCC = /usr/bin/gcc44# CPROF = -pg -gUSE_ZLIB = -DHAVE_ZLIBLZLIB = -lzUSE_GIFTI = -DHAVE_GIFTILGIFTI = /usr/lib64/libexpat.a# default to having these off# D_USE_ACML = -DUSE_ACML# I_USE_ACML = -I/opt/acml3.1.0/gnu64/include# L_USE_ACML = /opt/acml3.1.0/gnu64/lib/libacml.aCCDEBS = -DAFNI_DEBUG -DIMSEQ_DEBUG -DDISPLAY_DEBUG -DTHD_DEBUGCEXTRA = -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE # $(CPROF)CC = $(GCC) -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA)CCVOL = $(GCC) -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA)# CCFAST = $(GCC) -O2 -m64 -fPIC -DREAD_WRITE_64 -DLINUX2 $(CEXTRA)CCOLD = $(GCC)# The following line includes compiling for the SSE operations.# However, I found that it actually makes things worse in some test code.# Your mileage may vary.CCFAST = $(GCC) -O3 -mtune=generic -ffast-math -mmmx -msse -mfpmath=sse -DLINUX2 $(CEXTRA)CCMIN = $(GCC) -m64 -fPIC $(CPROF)CCD = $(GCC) $(CCDEBS)IFLAGS = -I. # -I/usr/X11R6/include $(I_USE_ACML)LFLAGS = -L. # -L/usr/X11R6/lib64 $(L_USE_ACML)# maybe CCSVD = $(GCC) -O0 -m64 -fPICPLUGIN_SUFFIX = soPLUGIN_LFLAGS = -shared -fPICPLUGIN_CC = $(GCC)# PLFLAGS = -rdynamic -L. -L/usr/X11R6/libPLFLAGS = -rdynamic -L. # -L/usr/X11R6/lib64SHOWOFF = -DSHOWOFF=linux_gcc4_64AR = /usr/bin/arRANLIB = /usr/bin/ranlibTAR = /bin/tarMKDIR = /bin/mkdirGZIP = /bin/gzipLD = $(GCC) $(CPROF)RM = /bin/rm -fMV = /bin/mv -fCP = /bin/cp -f# LINT = /usr/bin/lint -a -b -u -v -x $(IFLAGS) $(CCDEFS)INSTALLDIR = ../afni/linux_gcc44_64LIBDIR = $(INSTALLDIR)#INSTALL_PREREQ = sumaINSTALL_PREREQ = suma_gts# uncomment if the Gnu Scientific Library is installed (libgsl, libgslcblas)# GSLPROGS = balloonEXPROGS = gifti_tool $(GSLPROGS)# for dynamic linkingLLIBS = -lmri -lf2c -lXp -lXpm -lXext -lXmu -lXt $(LZLIB) $(LGIFTI) -lm -ldl -lc# for static linking to Motif, dynamic to all else# LLIBS = -lmri -lf2c /usr/X11R6/lib64/libXm.a -lXp -lXpm -lXext -lXmu -lXt -lSM -lICE -lX11 $(LZLIB) $(LGIFTI) -lm -ldl -lc# for static linking, as far as possible# LLIBS = -lmri -lf2c -ldl \# /usr/X11R6/lib/libXm.a \# /usr/X11R6/lib/libXpm.a \# /usr/X11R6/lib/libXext.a \# /usr/X11R6/lib/libXmu.a \# /usr/X11R6/lib/libXt.a \# /usr/X11R6/lib/libSM.a \# /usr/X11R6/lib/libICE.a \# /usr/X11R6/lib/libX11.a \# /usr/lib/libm.a \# /usr/lib/libc.a# vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv# For suma (NO STATIC LINKING OF GL libs)SUMA_GLIB_VER = -2.0SUMA_INCLUDE_PATH = -I./ -I../ -I../niml/ -Igts/src -I/usr/include/glib-1.2 -I/usr/include/glib-2.0 -I/usr/lib64/glib/include -I/usr/lib64/glib-2.0/includeSUMA_LINK_PATH = -L/usr/lib64 -L/usr/X11R6/lib64 -L../#use -lGLw if you have libGLw.a or libGLw.so* or # -lMesaGLw if you have Mesa's version (libMesaGLw*) of libGLwSUMA_LINK_LIB = -lGLw -lGLU -lGL -lXmu -lXp -lXt -lXext $(LZLIB) $(LGIFTI) -lm SUMA_MAKEFILE_NAME = SUMA_MakefileSUMA_BIN_ARCHIVE = SUMA_Linux.tar# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^###############################################################MAKE = makeinclude Makefile.INCLUDE |
Makefile.INCLUDE
#### Include for MCW AFNI make## -- goes at end of each platform specific Makefile.### for compiling with OpenMP, if availableCCOMP = $(CCFAST) $(OMPFLAG)EXINCOM = echo '..... Extra install commands (if any) .....' ; $(EXTRA_INSTALL_COMMANDS)F2C = f2c -A## 07 Dec 2005: modify the include flags hereINFLAGS = $(IFLAGS) -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr $(USE_ZLIB) $(USE_GIFTI)ISFLAGS = $(IFLAGS) -I../nifti/niftilib -I../nifti/nifticdf -I../nifti/znzlib -I../3DEdge/src -I../rickr $(USE_ZLIB)DOCS = ../doc/ps/*.ps ../doc/README/README* \ rickr/AFNI.changes.rickr rhammett/AFNI.changes.rhammett \ AFNI.changes.dglenMINDOCS = rickr/AFNI.changes.rickr AFNI.changes.dglenIMOBJS = display.o imseq.o bbox.o xim.o xutil.o LiteClue.o thd_xwebber.oAFOBJS = afni.o afni_func.o afni_widg.o afni_warp.o afni_fimmer.o \ afni_slice_short.o afni_slice_float.o afni_filer.o \ afni_slice_byte.o afni_slice_complex.o \ afni_pcor.o afni_pcor_float.o afni_transforms.o \ pbar.o afni_graph.o afni_plugin.o afni_cluster.o \ parser.o parser_int.o afni_plugout.o afni_fimfunc.o \ afni_setup.o afni_receive.o mcw_graf.o afni_splash.o \ afni_pplug_env.o afni_pplug_2dfunc.o afni_friends.o \ afni_ttren.o afni_pplug_1dfunc.o afni_driver.o \ afni_niml.o afni_sumafunc.o afni_slice_rgbyte.o \ afni_version.o afni_lock.o afni_vol2surf.o \ afni_pplug_instacorr.o afni_pplug_instacalc.oSOMEAFOBJS = parser_int.o afni_warp.o afni_slice_byte.o afni_slice_short.o \ afni_slice_float.o afni_slice_complex.o afni_slice_rgbyte.o \ parser.o pbar_color_defs.o afni_ports.oT3OBJS = to3d.oMISC = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.afnirc AFNI.sumarc \ 3d*.lib gmovie*## The following programs are "extras" not really part of the## 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 mycat $(EXPROGS)# mpegtoppm in above list## This list is the core AFNI package:## other programs are experimental and/or outsiders.PROGRAMS = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge count \ sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals \ fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3daxialize \ cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ 3dNLfim 3dTSgen AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \ 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ 2dImReg 3dmaskave 3dbuc2fim byteorder imstack 3dDeconvolve 3dTcat \ 3drotate 3dvolreg 3dpc 3dfractionize 1dplot adwarp imupsam \ 3dIntracranial 24swap 3dTsmooth RSFgen float_scan 1dtranspose \ 3dFourier 3dNotes 3dROIstats 1deval 3dStatClust 3dTstat 3dmaskdump \ 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dnorm afni_vcheck 3ddot \ 3dWavelets 3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign \ 3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \ 3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum \ 3dExtrema qhull strblast 3dConvolve 3dZcutup 3dZcat 3dTqual 3dGetrow \ 3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dCM fdrval \ 3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 3dAFNItoNIFTI \ 3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dAFNItoMINC 3dBrickStat \ 3dThreetoRGB Ifile 3dresample 3dAutobox 3dLRflip 3dANALYZEtoAFNI \ dicom_hdr 3dDespike dicom_to_raw file_tool rotcom 1ddot 1dsvd \ 3dDeconvolve_f 3dAnhist 3dAFNIto3D 3dUniformize 3dWarp nicat \ 3dSpatNorm fftest serial_helper 3dDTeig 3dDWItoDT 3dWarpDrive \ nifti_tool 3dAllineate nifti1_test whereami plugout_drive 3dLSS \ 3dMedianFilter 3dretroicor 3dAFNItoNIML 3dAFNItoRaw im2niml 3dedge3 \ DTIStudioFibertoSegments Dimon 3dLocalstat 3danisosmooth 3dmaxima \ 3dTwotoComplex 3dInvFMRI 3dmatcalc 3dAcost 3dLocalBistat 3dFWHMx \ 3dBlurToFWHM 1dSEM 3dDFT 3dSynthesize 1dMarry 3dEmpty 3dsvm \ 1dFlagMotion 3dTsort 1dTsort 3dTfitter afni_history 1dUpsample \ 3dLocalSVD niml_feedme 3dErrtsCormat 3dUndump 3dREMLfit 3dTnorm \ 3dUpsample 3dTcorrMap 3dmatmult 3dABoverlap 3dmaskSVD 1dBandpass \ 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip \ 3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D \ 3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI \ niccc rbox qdelaunay 3dkmeans 3dXYZcat 3dPolyfit 3dNwarpApply \ 1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo apsearch 1dBport \ 3dNormalityTest 3dmask_tool FIRdesign help_format 2perm 3dClustCount \ column_cat $(EXTRAS)PROGRAMS_NOPLUG = afni to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \ sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnoise count \ fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim imupsam \ cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 3drefit \ waver 3dnewid 3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval \ 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ imstack byteorder 3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot \ 24swap 3dTsmooth RSFgen float_scan 3dDeconvolve_f 1ddot 1dsvd \ 3dFourier 3dNotes 3dROIstats 1deval 3dStatClust 3dTstat 3ddelay \ 3dDTeig 3dDWItoDT 1dtranspose whereami 3dAFNItoNIML 3dcopy imcat \ 3dDetrend 1dfft 3drename 1dnorm afni_vcheck 3ddot 3dBrickStat \ imcutup 3dMean 3dAttribute 3dZeropad 3dWinsor 3dmaskdump 3dfim+ \ 3dUndump cat_matvec 3dOverlap 3dClipLevel 3dZregrid 3dEntropy \ ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum 3dExtrema strblast \ 3dConvolve 3dZcutup 3dZcat 3dTqual 3dTcorrelate 3dAnatNudge \ Vecwarp 3dMINCtoAFNI 3dAFNItoANALYZE 3dAFNItoNIFTI siemens_vision \ mayo_analyze 3dAutoTcorrelate 3dFDR 3dAutomask 3dAFNItoMINC \ 3dThreetoRGB Ifile 3dresample 3dAutobox 3dLRflip 3dANALYZEtoAFNI \ dicom_hdr 3dDespike dicom_to_raw file_tool rotcom 3dUniformize \ 3dWarp nicat 3dSpatNorm 3dWarpDrive 3dretroicor ge_header 3dTnorm \ 3dAFNItoRaw DTIStudioFibertoSegments im2niml 3dLocalstat 3dGetrow \ nifti_tool 3dAllineate nifti1_test Dimon 3danisosmooth \ 3dmaxima 3dTwotoComplex 3dInvFMRI 1dmatcalc 3dmatcalc 3dAcost \ 3dLocalBistat 3dFWHMx 3dBlurToFWHM 1dSEM 3dDFT 3dSynthesize \ 1dMarry 3dEmpty 3dTsort 1dTsort 1dFlagMotion 3dTfitter 1dBport \ 3dLocalSVD 3dFFT 1dcat 3dErrtsCormat 3dREMLfit 3dTcorrMap \ afni_history 3dUpsample 1dUpsample 3dmatmult 3dABoverlap \ 3dmaskSVD 3dRank 3dLocalPV 3dTcorr1D 3dClustSim 3dRetinoPhase \ 3dMaskToASCII 3dttest++ 3dDTtoDWI niccc 3dXYZcat 3dPolyfit \ 3dNwarpApply 1dCorrelate 3dCountSpikes 3dNwarpCalc dicom_hinfo \ apsearch 3dNormalityTest 3dmask_tool 2perm 3dClustCount \ $(EXTRAS)# For CYGWIN (look for "exe" to find various places below)# Note that 3dNLfim and 3dTSgen are missing for nowPROGRAMS_EXE = afni.exe to3d from3d abut 3dclust nsize 3dinfo 3dproject 3dmerge \ sfim tfim ftosh 3dttest 3ddup imrotate imreg imstat 3dnvals count \ fim2 imand FD2 sqwave immask imdump imaver 3dhistog 3dfim 3dGetrow \ cdf 2swap 4swap mritopgm 3dANOVA 3dANOVA2 3dANOVA3 plugout_tta \ waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket \ 3dAFNItoNIML AlphaSim 3dFWHM plugout_tt 3dnoise plugout_ijk \ 3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna \ 2dImReg 3dmaskave 3dbuc2fim byteorder imstack 3dDeconvolve 3dTcat \ 3drotate 3dvolreg 3dpc 3dfractionize 1dplot adwarp imupsam 1dBport \ 3dIntracranial 24swap 3dTsmooth RSFgen float_scan 1dtranspose \ 3dFourier 3dNotes 3dROIstats 1deval 3dStatClust 1ddot 3dBrickStat \ 3dDWItoDT 3dTstat 3dDTeig 3dmaskdump 3dretroicor 3daxialize imcat \ 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dnorm afni_vcheck 3ddot \ 3dWavelets 3dfim+ imcutup 3dWinsor 3dZeropad 3dTagalign 3dUndump \ 3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid \ 3dEntropy 3ddelay ent16 3dRowFillin 1dgrayplot 3dToutcount 1dsum \ 3dExtrema qhull.exe strblast 3dConvolve 3dZcutup 3dZcat 3dTqual \ 3dTcorrelate 3dAnatNudge 3dcopy Vecwarp 3dMINCtoAFNI 3dAFNItoNIFTI \ 3dAFNItoANALYZE siemens_vision ge_header mayo_analyze 1dsvd \ 3dAutoTcorrelate 3dFDR 3dAutomask 3dAFNItoMINC 3dThreetoRGB Ifile \ 3dAutobox 3dLRflip 3dANALYZEtoAFNI dicom_hdr 3dDespike nicat \ dicom_to_raw rotcom 3dDeconvolve_f 3dUniformize 3dWarp 3dWarpDrive \ file_tool 3dresample serial_helper im2niml 3dUpsample \ nifti_tool 3dAFNItoRaw DTIStudioFibertoSegments Dimon 3dREMLfit \ 3danisosmooth 3dTwotoComplex 3dInvFMRI 3dmatcalc 3dAllineate \ 3dFWHMx 3dBlurToFWHM 1dSEM 3dDFT 3dSynthesize 1dMarry 3dEmpty \ 1dFlagMotion 3dTsort 1dTsort 3dTfitter afni_history 1dUpsample \ 3dTcorrMap 3dABoverlap 3dRank 3dFFT 3dTcorr1D 3dClustSim \ 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI niccc 3dXYZcat \ column_catSCRIPTS = @4Daverage @CommandGlobb @GetAfniOrient @DTI_studio_reposition \ @GetAfniPrefix @NoExt @UpdateAfni @RenamePanga @2dwarper \ @GetAfniView @SUMA_AlignToExperiment @SUMA_Make_Spec_FS @Purify_1D \ @SUMA_Make_Spec_SF @make_stim_file @Align_Centers suma_change_spec \ @CheckForAfniDset @clip_volume @AfniOrient2RAImap @parse_afni_name \ @auto_align @auto_tlrc @FromRAI @ToRAI @AfniOrientSign @VolCenter \ @Center_Distance @fix_FSsphere @parse_name @align_partial_oblique \ @np 3dMax @IsoMasks @SUMA_Make_Spec_Caret @FindAfniDsetPath @GetAfniID \ @float_fix @escape- 3dPAR2AFNI.pl @DriveAfni @DriveSuma @AddEdge \ @SurfSmooth.HEAT_07.examples @SUMA_FSvolToBRIK @isOblique afni_run_R \ @GetAfniDims @GetAfniRes @NoisySkullStrip @statauxcode @ScaleVolume \ @ShowDynamicRange AFNI_Batch_R @DO.examples demo.fixed.niml.do \ demo.mobile.niml.do @Spharm.examples @GetAfniBin @fast_roi \ @make_plug_diff @build_afni_Xlib @update.afni.binaries @ROI_Corr_Mat \ @FS_roi_label @demo_prompt @ScriptCheck @NoPound @Reorder 3dSignatures \ 3dMEMA @DiceMetric @R_funclist @TimeDiff @FullPath @RetinoProc \ @ANATICOR @MakeLabelTable @ElectroGrid ExamineXmat 1dRplot \ @2dwarper.Allin @Shift_Volume @help.AFNI @1dDiffMag @FSlabel2dset \ @Install_InstaCorr_Demo @Quiet_Talkers @radial_correlate \ @DeblankFileNames @clean_help_dir @global_parse @AfniEnv @Atlasize \ @Install_TSrestMovieDemo @Install_AfniRetinoDemo \ @Install_PTaylor_TractDemo @Install_RSFMRI_Motion_Group_Demo \ @Install_MEICA_Demo @T1scale 3dMVM PY_DIR = python_scriptsPY_SCRIPTS = afni_base.py @DoPerRoi.pyR_DIR = R_scriptsLIBHEADERS = mrilib.h mcw_glob.h 3ddata.h thd_maker.h thd_iochan.h \ editvol.h cs.h eispack.h killer.h vecmat.h machdep.h tagset.h \ thd_compress.h afni_warp.h coxplot.h f2c.h volpack.h mcw_malloc.h\ multivector.h afni_environ.h niml.h cs_sort_template.h vol2surf.h\ AFNI_label.h Amalloc.h afni_suma.h debugtrace.h list_struct.h \ mri_dicom_stuff.h mri_warpfield.h nifti/niftilib/nifti1.h \ nifti/niftilib/nifti1_io.h nifti/nifticdf/nifticdf.h \ nifti/znzlib/znzlib.h \ rickr/r_new_resam_dset.h rickr/r_idisp.h rickr/r_misc.h### Make everything, install it too, and cleanuptotality:clean all plugins install install_plugins install_lib cleann### Make everything, install it too, but don't cleanupvastness:all plugins install install_plugins install_lib### Make many thingsall:$(LIBDL) libmri.a libmrix.a libcoxplot.a libvolpack.a libtracktools.a \ R_io.so programs ptaylor_all### Make afni binariesafobj:$(AFOBJS) libf2c.a libcoxplot.a libvolpack.a libmrix.a libjpeg.a libXmHTML.aafobjs: afobj### Make a few more thingsitall:all plugins install install_plugins$(INSTALLDIR): if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo Made directory $(INSTALLDIR); fi### for those on crippled systemsall_noplug:libmri.a libmrix.a libcoxplot.a programs_noplugtotality_noplug:libmri.a libmrix.a libcoxplot.a programs_noplug install_noplug clean# CYGWIN: variations on totality and vastness abovetotality_exe:libmri.a libmrix.a libcoxplot.a programs_exe install_exe clean_exevastness_exe:libmri.a libmrix.a libcoxplot.a programs_exe install_exeprograms:$(PROGRAMS)programs_noplug:$(PROGRAMS_NOPLUG)programs_exe:$(PROGRAMS_EXE)libraries:libmri.a libmrix.a libcoxplot.a libvolpack.a libf2c.a### rules for individual programsquotize:quotize.o $(CC) -o quotize quotize.o $(LFLAGS) $(LLIBS)license.h:../doc/README/README.copyright quotize license < ../doc/README/README.copyright > license.hreadmes:readme_env.h readme_afnigui.hreadme_env.h:../doc/README/README.environment quotize readme_env < ../doc/README/README.environment > readme_env.hreadme_afnigui.h:../doc/README/README.afnigui quotize readme_afnigui < ../doc/README/README.afnigui > readme_afnigui.hIfile:Ifile.o $(CC) -o Ifile Ifile.o $(LFLAGS) $(LLIBS)3dHmetric:3dHmetric.o $(CC) -o 3dHmetric 3dHmetric.o $(LFLAGS) $(LLIBS)3dJointHist:3dJointHist.o $(CC) -o 3dJointHist 3dJointHist.o $(LFLAGS) $(LLIBS)3dUndump:3dUndump.o $(CC) -o 3dUndump 3dUndump.o $(LFLAGS) $(LLIBS)3dGetrow:3dGetrow.o $(CC) -o 3dGetrow 3dGetrow.o $(LFLAGS) $(LLIBS)3dnoise:3dnoise.o $(CC) -o 3dnoise 3dnoise.o $(LFLAGS) $(LLIBS)3dstrip:3dstrip.o $(CC) -o 3dstrip 3dstrip.o $(LFLAGS) $(LLIBS)byteorder:byteorder.o $(CC) -o byteorder byteorder.o $(LFLAGS) $(LLIBS)3dbuc2fim:3dbuc2fim.o $(CC) -o 3dbuc2fim 3dbuc2fim.o $(LFLAGS) $(LLIBS)mritopgm:mritopgm.c $(CC) -o mritopgm mritopgm.c $(INFLAGS) $(LFLAGS) $(LLIBS)ppmtocmap:ppmtocmap.c $(CC) -o ppmtocmap ppmtocmap.c $(INFLAGS) $(LFLAGS) $(LLIBS)impdif:impdif.c $(CC) -o impdif impdif.c $(INFLAGS) $(LFLAGS) $(LLIBS)imcutup:imcutup.c $(CC) -o imcutup imcutup.c $(INFLAGS) $(LFLAGS) $(LLIBS)imcat:imcat.c $(CC) -o imcat imcat.c $(INFLAGS) $(LFLAGS) $(LLIBS)Vecwarp:Vecwarp.c $(CC) -o Vecwarp Vecwarp.c $(INFLAGS) $(LFLAGS) $(LLIBS)float_scan:float_scan.c $(CC) -o float_scan float_scan.c $(INFLAGS) $(LFLAGS) $(LLIBS)to26:to26.c $(CC) -o to26 to26.c $(INFLAGS) $(LFLAGS) $(LLIBS)toxx:toxx.c $(CC) -o toxx toxx.c $(INFLAGS) $(LFLAGS) $(LLIBS)imupsam:imupsam.c $(CC) -o imupsam imupsam.c $(INFLAGS) $(LFLAGS) $(LLIBS)2swap:2swap.c $(CC) -o 2swap 2swap.c $(INFLAGS) $(LFLAGS) $(LLIBS)4swap:4swap.c $(CC) -o 4swap 4swap.c $(INFLAGS) $(LFLAGS) $(LLIBS)24swap:24swap.c $(CC) -o 24swap 24swap.c $(INFLAGS) $(LFLAGS) $(LLIBS)crao:crao.o $(CC) -o crao crao.o $(LFLAGS) $(LLIBS)crao2:crao2.o $(CC) -o crao2 crao2.o $(LFLAGS) $(LLIBS)imaver:imaver.o $(CC) -o imaver imaver.o $(LFLAGS) $(LLIBS)impsd:impsd.o $(CC) -o impsd impsd.o $(LFLAGS) $(LLIBS)zfuntest:zfuntest.o $(CC) -o zfuntest zfuntest.o $(LFLAGS) $(LLIBS)imdump:imdump.o $(CC) -o imdump imdump.o $(LFLAGS) $(LLIBS)im2niml:im2niml.o $(CC) -o im2niml im2niml.o $(LFLAGS) $(LLIBS)imswap:imswap.o $(CC) -o imswap imswap.o $(LFLAGS) $(LLIBS)immask:immask.o $(CC) -o immask immask.o $(LFLAGS) $(LLIBS)sqwave:sqwave.o $(CC) -o sqwave sqwave.opcor.o:pcor.c pcor.h $(RM) $@ $(CC) -c pcor.c $(INFLAGS) -DREF_FLOAT_SINGLE -UVOX_SHORTpcorsh.o:pcor.c pcor.h $(RM) $@ $(CP) pcor.c pcorsh.c $(CC) -c pcorsh.c $(INFLAGS) -DREF_FLOAT_SINGLE -DVOX_SHORT $(RM) pcorsh.c# FD2:FD2.o ts.o mcw.o overfim.o pcorsh.o csfft_AJ.o# $(RM) $@# $(CC) -o FD2 FD2.o mcw.o overfim.o ts.o pcorsh.o csfft_AJ.o $(LFLAGS) $(LLIBS)FD2.o:FD2.c FD2_inc.cFD2:FD2.o ts.o mcw.o overfim.o pcorsh.o csfft_AJ.o FD2_inc.c $(RM) $@ $(CC) -o FD2 FD2.o mcw.o overfim.o ts.o pcorsh.o csfft_AJ.o $(LFLAGS) -lX11 -lm -lcdFD2:dFD2.o ts.o mcw.o overfim.o pcorsh.o $(RM) $@ $(CC) -o dFD2 dFD2.o mcw.o overfim.o ts.o pcorsh.o $(LFLAGS) $(LLIBS)fim:fim.c $(RM) $@ $(CC) -o fim fim.c -DSYSV $(LFLAGS) $(LLIBS)bzip2:bzip2.o $(CC) -o bzip2 bzip2.ofim2:fim2.o ts.o pcor.o $(RM) $@ $(CC) -o fim2 fim2.o ts.o pcor.o $(LFLAGS) $(LLIBS)imstat:imstat.o $(RM) $@ $(CC) -o imstat imstat.o $(LFLAGS) $(LLIBS)imstack:imstack.o $(RM) $@ $(CC) -o imstack imstack.o $(LFLAGS) $(LLIBS)imreg:imreg.o pcor.o $(RM) $@ $(CC) -o imreg imreg.o pcor.o $(LFLAGS) $(LLIBS)FIRdesign.o:FIRdesign.c remez.c remez.hFIRdesign:FIRdesign.o $(RM) $@ $(CC) -o FIRdesign FIRdesign.o $(LFLAGS) $(LLIBS)imfit:imfit.o $(RM) $@ $(CC) -o imfit imfit.o $(LFLAGS) $(LLIBS)imand:imand.o $(RM) $@ $(CC) -o imand imand.o $(LFLAGS) $(LLIBS)imrotate:imrotate.o $(RM) $@ $(CC) -o imrotate imrotate.o $(LFLAGS) $(LLIBS)dsetdup:dsetdup.o $(RM) $@ $(CC) -o dsetdup dsetdup.o $(LFLAGS) $(LLIBS)3ddup:3ddup.o $(RM) $@ $(CC) -o 3ddup 3ddup.o $(LFLAGS) $(LLIBS)3dZeropad:3dZeropad.o $(RM) $@ $(CC) -o 3dZeropad 3dZeropad.o $(LFLAGS) $(LLIBS)3dnvals:3dnvals.o $(RM) $@ $(CC) -o 3dnvals 3dnvals.o $(LFLAGS) $(LLIBS)3dAttribute:3dAttribute.o $(RM) $@ $(CC) -o 3dAttribute 3dAttribute.o $(LFLAGS) $(LLIBS)3dproject:3dproject.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dproject 3dproject.o parser.o parser_int.o \ $(LFLAGS) $(LLIBS)3dinfo:3dinfo.o $(RM) $@ $(CC) -o 3dinfo 3dinfo.o $(LFLAGS) $(LLIBS)3dmaskave:3dmaskave.o $(RM) $@ $(CC) -o 3dmaskave 3dmaskave.o $(LFLAGS) $(LLIBS)3dmaskdump:3dmaskdump.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dmaskdump 3dmaskdump.o parser.o parser_int.o \ $(LFLAGS) $(LLIBS)3drefit:3drefit.o $(RM) $@ $(CC) -o 3drefit 3drefit.o $(LFLAGS) $(LLIBS)3drename:3drename.o $(RM) $@ $(CC) -o 3drename 3drename.o $(LFLAGS) $(LLIBS)3dcopy:3dcopy.o $(RM) $@ $(CC) -o 3dcopy 3dcopy.o $(LFLAGS) $(LLIBS)3daxialize:3daxialize.o $(RM) $@ $(CC) -o 3daxialize 3daxialize.o $(LFLAGS) $(LLIBS)3dfractionize:3dfractionize.o $(RM) $@ $(CC) -o 3dfractionize 3dfractionize.o $(LFLAGS) $(LLIBS)3dbucket:3dbucket.o $(RM) $@ $(CC) -o 3dbucket 3dbucket.o $(LFLAGS) $(LLIBS)3dZcutup:3dZcutup.o $(RM) $@ $(CC) -o 3dZcutup 3dZcutup.o $(LFLAGS) $(LLIBS)3dZcat:3dZcat.o $(RM) $@ $(CC) -o 3dZcat 3dZcat.o $(LFLAGS) $(LLIBS)3dXYZcat:3dXYZcat.o $(RM) $@ $(CC) -o 3dXYZcat 3dXYZcat.o $(LFLAGS) $(LLIBS)3dTqual:3dTqual.o $(RM) $@ $(CC) -o 3dTqual 3dTqual.o $(LFLAGS) $(LLIBS)3dTcat:3dTcat.o $(RM) $@ $(CC) -o 3dTcat 3dTcat.o $(LFLAGS) $(LLIBS)3dSynthesize:3dSynthesize.o $(RM) $@ $(CC) -o 3dSynthesize 3dSynthesize.o $(LFLAGS) $(LLIBS)3dTcorrelate:3dTcorrelate.o $(RM) $@ $(CC) -o 3dTcorrelate 3dTcorrelate.o $(LFLAGS) $(LLIBS)3dTagalign:3dTagalign.o $(RM) $@ $(CC) -o 3dTagalign 3dTagalign.o $(LFLAGS) $(LLIBS)3dTshift:3dTshift.o $(RM) $@ $(CC) -o 3dTshift 3dTshift.o $(LFLAGS) $(LLIBS)3dTnorm:3dTnorm.o $(RM) $@ $(CC) -o 3dTnorm 3dTnorm.o $(LFLAGS) $(LLIBS)3dTstat:3dTstat.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dTstat 3dTstat.o parser.o parser_int.o $(LFLAGS) \ $(LLIBS)3dTfitter:3dTfitter.o thd_fitter.o thd_lasso.o $(RM) $@ $(CC) -o 3dTfitter 3dTfitter.o $(LFLAGS) $(LLIBS)3dTsort:3dTsort.o $(RM) $@ $(CC) -o 3dTsort 3dTsort.o $(LFLAGS) $(LLIBS)3dPeriodogram:3dPeriodogram.o $(RM) $@ $(CC) -o 3dPeriodogram 3dPeriodogram.o $(LFLAGS) $(LLIBS)1dAstrip:1dAstrip.o $(RM) $@ $(CC) -o 1dAstrip 1dAstrip.o1dBport.o:1dBport.c mri_bport.c1dBport:1dBport.o $(RM) $@ $(CC) -o 1dBport 1dBport.o $(LFLAGS) $(LLIBS)3dLocalBistat:3dLocalBistat.o $(RM) $@ $(CC) -o 3dLocalBistat 3dLocalBistat.o $(LFLAGS) $(LLIBS)3dmaskSVD:3dmaskSVD.o $(RM) $@ $(CC) -o 3dmaskSVD 3dmaskSVD.o $(LFLAGS) $(LLIBS)3dBlurToFWHM:3dBlurToFWHM.o $(RM) $@ $(CCFAST) -o 3dBlurToFWHM 3dBlurToFWHM.o $(LFLAGS) $(LLIBS)3dDFT:3dDFT.o $(RM) $@ $(CC) -o 3dDFT 3dDFT.o $(LFLAGS) $(LLIBS)3dRetinoPhase:3dRetinoPhase.o $(RM) $@ $(CC) -o 3dRetinoPhase 3dRetinoPhase.o $(LFLAGS) $(LLIBS)3dDTeig:3dDTeig.o libmri.a $(RM) $@ $(CC) -o 3dDTeig 3dDTeig.o $(LFLAGS) $(LLIBS)3dDWItoDT:3dDWItoDT.o libmri.a $(RM) $@ $(CC) -o 3dDWItoDT 3dDWItoDT.o $(LFLAGS) $(LLIBS)1dSEM:1dSEM.o libmri.a sqrmat.o matrix.c matrix.h $(RM) $@ $(CC) -o 1dSEM 1dSEM.o sqrmat.o $(LFLAGS) $(LLIBS)3dDTtoDWI:3dDTtoDWI.o libmri.a $(RM) $@ $(CC) -o 3dDTtoDWI 3dDTtoDWI.o $(LFLAGS) $(LLIBS)3danisosmooth:3danisosmooth.o DWIstructtensor.o libmri.a $(RM) $@ $(CCFAST) -o 3danisosmooth 3danisosmooth.o DWIstructtensor.o \ $(LFLAGS) $(LLIBS) 3dToutcount:3dToutcount.o $(RM) $@ $(CC) -o 3dToutcount 3dToutcount.o $(LFLAGS) $(LLIBS) 3dCountSpikes:3dCountSpikes.o $(RM) $@ $(CC) -o 3dCountSpikes 3dCountSpikes.o $(LFLAGS) $(LLIBS)3dTsmooth:3dTsmooth.o $(RM) $@ $(CC) -o 3dTsmooth 3dTsmooth.o $(LFLAGS) $(LLIBS)3dMean:3dMean.o $(RM) $@ $(CC) -o 3dMean 3dMean.o $(LFLAGS) $(LLIBS)3dBrickStat:3dBrickStat.o $(RM) $@ $(CC) -o 3dBrickStat 3dBrickStat.o $(LFLAGS) $(LLIBS)3dMINCtoAFNI:3dMINCtoAFNI.o $(RM) $@ $(CC) -o 3dMINCtoAFNI 3dMINCtoAFNI.o $(LFLAGS) $(LLIBS)3dAFNItoMINC:3dAFNItoMINC.o $(RM) $@ $(CC) -o 3dAFNItoMINC 3dAFNItoMINC.o $(LFLAGS) $(LLIBS)3dAFNItoRaw:3dAFNItoRaw.o $(RM) $@ $(CC) -o 3dAFNItoRaw 3dAFNItoRaw.o $(LFLAGS) $(LLIBS)3dAFNItoNIML:3dAFNItoNIML.o $(RM) $@ $(CC) -o 3dAFNItoNIML 3dAFNItoNIML.o $(LFLAGS) $(LLIBS)3dAFNIto3D:3dAFNIto3D.o $(RM) $@ $(CC) -o 3dAFNIto3D 3dAFNIto3D.o $(LFLAGS) $(LLIBS)3dAFNItoANALYZE:3dAFNItoANALYZE.o $(RM) $@ $(CC) -o 3dAFNItoANALYZE 3dAFNItoANALYZE.o $(LFLAGS) $(LLIBS)3dANALYZEtoAFNI:3dANALYZEtoAFNI.o $(RM) $@ $(CC) -o 3dANALYZEtoAFNI 3dANALYZEtoAFNI.o $(LFLAGS) $(LLIBS)3dThreetoRGB:3dThreetoRGB.o $(RM) $@ $(CC) -o 3dThreetoRGB 3dThreetoRGB.o $(LFLAGS) $(LLIBS)3dTwotoComplex:3dTwotoComplex.o $(RM) $@ $(CC) -o 3dTwotoComplex 3dTwotoComplex.o $(LFLAGS) $(LLIBS)3dInvFMRI:3dInvFMRI.o $(RM) $@ $(CC) -o 3dInvFMRI 3dInvFMRI.o $(LFLAGS) $(LLIBS)3dvolreg:3dvolreg.o $(RM) $@ $(CC) -o 3dvolreg 3dvolreg.o $(LFLAGS) $(LLIBS)3dedge:3dedge.o $(RM) $@ $(CC) -o 3dedge 3dedge.o $(LFLAGS) $(LLIBS)from3d:from3d.o $(RM) $@ $(CC) -o from3d from3d.o $(LFLAGS) $(LLIBS)3dfim:3dfim.o afni_pcor_float.o ts.o $(RM) $@ $(CC) -o 3dfim 3dfim.o ts.o afni_pcor_float.o $(LFLAGS) $(LLIBS)3T_toafni:3T_toafni.o $(RM) $@ $(CC) -o 3T_toafni 3T_toafni.o $(LFLAGS) $(LLIBS)3dRank:3dRank.o $(RM) $@ $(CC) -o 3dRank 3dRank.o $(LFLAGS) $(LLIBS)3dRankizer:3dRankizer.o $(RM) $@ $(CC) -o 3dRankizer 3dRankizer.o $(LFLAGS) $(LLIBS)p2t:p2t.o $(RM) $@ $(CC) -o p2t p2t.o $(LFLAGS) $(LLIBS)cdf:cdf.o $(RM) $@ $(CC) -o cdf cdf.o $(LFLAGS) $(LLIBS)fdrval:fdrval.o $(RM) $@ $(CC) -o fdrval fdrval.o $(LFLAGS) $(LLIBS)hide:hide.o $(RM) $@ $(CC) -o hide hide.o $(LFLAGS)count:count.o $(RM) $@ $(CC) -o count count.o $(LFLAGS) $(LLIBS)nsize:nsize.o $(RM) $@ $(CC) -o nsize nsize.o $(LFLAGS) $(LLIBS)3dclust:3dclust.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dclust 3dclust.o parser.o parser_int.o \ $(LFLAGS) $(LLIBS)3dhistog:3dhistog.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dhistog 3dhistog.o parser.o parser_int.o \ $(LFLAGS) $(LLIBS)3dAnhist:3dAnhist.o $(RM) $@ $(CC) -o 3dAnhist 3dAnhist.o $(LFLAGS) $(LLIBS)3dhclip:3dhclip.o $(RM) $@ $(CC) -o 3dhclip 3dhclip.o $(LFLAGS) $(LLIBS)3dErrtsCormat:3dErrtsCormat.o $(RM) $@ $(CC) -o 3dErrtsCormat 3dErrtsCormat.o $(LFLAGS) $(LLIBS)3dLocalCormat:3dLocalCormat.o $(RM) $@ $(CC) -o 3dLocalCormat 3dLocalCormat.o $(LFLAGS) $(LLIBS)3dmerge:3dmerge.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dmerge 3dmerge.o parser.o parser_int.o \ $(LFLAGS) $(LLIBS)3dcalc:3dcalc.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dcalc 3dcalc.o parser.o parser_int.o \ $(LFLAGS) $(LLIBS)3dDetrend:3dDetrend.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dDetrend 3dDetrend.o parser.o parser_int.o \ $(LFLAGS) $(LLIBS)d3dmerge:3dmerge.c $(RM) $@ $(CCD) -o d3dmerge 3dmerge.c $(LFLAGS) $(LLIBS)3dttest:3dttest.o parser.o parser_int.o $(RM) $@ $(CC) -o 3dttest 3dttest.o parser.o parser_int.o $(LFLAGS) $(LLIBS)3dttest++:3dttest++.o $(RM) $@ $(CC) -o 3dttest++ 3dttest++.o $(LFLAGS) $(LLIBS)3dedge3:lib3DEdge.a 3dedge3.o $(RM) $@ $(CC) -o 3dedge3 3dedge3.o -I3DEdge/src \ $(LFLAGS) -l3DEdge $(LLIBS)### From Stephen LaConte3dsvm: ( cd svm/ ; \ $(CC) -o 3dsvm 3dsvm_common.c svm_common.c svm_learn.c \ svm_hideo.c 3dsvm.c \ -I.. $(ISFLAGS) -L.. $(LFLAGS) $(LLIBS) -lf2c -lmri ; \ $(MV) 3dsvm ../. ; \ cd .. ;)whereami:whereami.c $(RM) $@ $(CC) -o whereami whereami.c parser.o parser_int.o $(INFLAGS) $(LFLAGS) $(LLIBS)apsearch:apsearch.c $(RM) $@ $(CC) -o apsearch apsearch.c $(INFLAGS) $(LFLAGS) $(LLIBS)3dSegment:3dSegment.c $(RM) $@ $(CC) -o 3dSegment 3dSegment.c parser.o parser_int.o $(INFLAGS) $(LFLAGS) $(LLIBS)3dUniformize:3dUniformize.o $(RM) $@ $(CC) -o 3dUniformize 3dUniformize.o $(PLFLAGS) $(LLIBS)3dpc:3dpc.o $(RM) $@ $(CC) -o 3dpc 3dpc.o $(LFLAGS) $(LLIBS)3duca:3duca.o $(RM) $@ $(CC) -o 3duca 3duca.o $(LFLAGS) $(LLIBS)3duuu:3duuu.o uuu.c $(RM) $@ $(CC) -o 3duuu 3duuu.o $(LFLAGS) $(LLIBS)3duuu2:3duuu2.o uuu2.c $(RM) $@ $(CC) -o 3duuu2 3duuu2.o $(LFLAGS) $(LLIBS)3ddot:3ddot.o $(RM) $@ $(CC) -o 3ddot 3ddot.o $(LFLAGS) $(LLIBS)3dPaxes:3dPaxes.o $(RM) $@ $(CC) -o 3dPaxes 3dPaxes.o $(LFLAGS) $(LLIBS)3dRowFillin:3dRowFillin.o $(RM) $@ $(CC) -o 3dRowFillin 3dRowFillin.o $(LFLAGS) $(LLIBS)3dZFillin:3dZFillin.o $(RM) $@ $(CC) -o 3dZFillin 3dZFillin.o $(LFLAGS) $(LLIBS)3ddelay:3ddelay.o $(RM) $@ $(CC) -o 3ddelay 3ddelay.o $(LFLAGS) $(LLIBS)ent16:ent16.o $(RM) $@ $(CC) -o ent16 ent16.o $(LFLAGS) $(LLIBS)strblast:strblast.o $(RM) $@ $(CC) -o strblast strblast.o $(LFLAGS) $(LLIBS)3dEntropy:3dEntropy.o $(RM) $@ $(CC) -o 3dEntropy 3dEntropy.o $(LFLAGS) $(LLIBS)3dZregrid:3dZregrid.o $(RM) $@ $(CC) -o 3dZregrid 3dZregrid.o $(LFLAGS) $(LLIBS)3dOverlap:3dOverlap.o $(RM) $@ $(CC) -o 3dOverlap 3dOverlap.o $(LFLAGS) $(LLIBS)3dABoverlap:3dABoverlap.o $(RM) $@ $(CC) -o 3dABoverlap 3dABoverlap.o $(LFLAGS) $(LLIBS)3dNormalityTest.o:3dNormalityTest.c $(RM) $@ $(CCFAST) -c 3dNormalityTest.c $(INFLAGS)3dNormalityTest:3dNormalityTest.o $(RM) $@ $(CCFAST) -o 3dNormalityTest 3dNormalityTest.o $(LFLAGS) $(LLIBS)3dClipLevel:3dClipLevel.o $(RM) $@ $(CC) -o 3dClipLevel 3dClipLevel.o $(LFLAGS) $(LLIBS)3dAutomask:3dAutomask.o $(RM) $@ $(CC) -o 3dAutomask 3dAutomask.o $(LFLAGS) $(LLIBS)3dLRflip:3dLRflip.o $(RM) $@ $(CC) -o 3dLRflip 3dLRflip.o $(LFLAGS) $(LLIBS)3dAutobox:3dAutobox.o $(RM) $@ $(CC) -o 3dAutobox 3dAutobox.o $(LFLAGS) $(LLIBS)3dWinsor:3dWinsor.o $(RM) $@ $(CC) -o 3dWinsor 3dWinsor.o $(LFLAGS) $(LLIBS)3dMedianFilter:3dMedianFilter.o $(RM) $@ $(CC) -o 3dMedianFilter 3dMedianFilter.o $(LFLAGS) $(LLIBS)3dPolyfit:3dPolyfit.o $(RM) $@ $(CC) -o 3dPolyfit 3dPolyfit.o $(LFLAGS) $(LLIBS)3drotate:3drotate.o $(RM) $@ $(CC) -o 3drotate 3drotate.o $(LFLAGS) $(LLIBS)3dWarp:3dWarp.o $(RM) $@ $(CC) -o 3dWarp 3dWarp.o $(LFLAGS) $(LLIBS)3dWarpDrive:3dWarpDrive.o $(RM) $@ $(CC) -o 3dWarpDrive 3dWarpDrive.o $(LFLAGS) $(LLIBS)qm:qm.o $(RM) $@ $(CC) -o qm qm.o $(LFLAGS) $(LLIBS)3dAcost:3dAcost.o $(RM) $@ $(CCFAST) -o 3dAcost 3dAcost.o $(LFLAGS) $(LLIBS)3dSetupGroupInCorr.o:3dSetupGroupInCorr.c $(RM) $@ $(CCFAST) -c 3dSetupGroupInCorr.c $(INFLAGS)3dSetupGroupInCorr:3dSetupGroupInCorr.o $(RM) $@ $(CCFAST) -o 3dSetupGroupInCorr 3dSetupGroupInCorr.o $(LFLAGS) $(LLIBS)3dTransformGroupInCorr:3dTransformGroupInCorr.o $(RM) $@ $(CCFAST) -o 3dTransformGroupInCorr 3dTransformGroupInCorr.o $(LFLAGS) $(LLIBS)3dExtractGroupInCorr:3dExtractGroupInCorr.o $(RM) $@ $(CCFAST) -o 3dExtractGroupInCorr 3dExtractGroupInCorr.o $(LFLAGS) $(LLIBS)rotcom:rotcom.o $(RM) $@ $(CC) -o rotcom rotcom.o $(LFLAGS) $(LLIBS)3dDistize:3dDistize.o $(RM) $@ $(CC) -o 3dDistize 3dDistize.o $(LFLAGS) $(LLIBS)3dDimize:3dDimize.o $(RM) $@ $(CC) -o 3dDimize 3dDimize.o $(LFLAGS) $(LLIBS)3dAnatNudge:3dAnatNudge.o $(RM) $@ $(CC) -o 3dAnatNudge 3dAnatNudge.o $(LFLAGS) $(LLIBS)rtfeedme:rtfeedme.o $(RM) $@ $(CC) -o rtfeedme rtfeedme.o $(LFLAGS) $(LLIBS)niml_feedme:niml_feedme.o $(RM) $@ $(CC) -o niml_feedme niml_feedme.o $(LFLAGS) $(LLIBS)3dFDR:3dFDR.o $(RM) $@ $(CC) -o 3dFDR 3dFDR.o $(LFLAGS) $(LLIBS)3dANOVA.o: 3dANOVA.lib3dANOVA2.o:3dANOVA.lib3dANOVA3.o:3dANOVA.lib3dANOVA:3dANOVA.o $(RM) $@ $(CC) -o 3dANOVA 3dANOVA.o $(LFLAGS) $(LLIBS)3dANOVA2:3dANOVA2.o $(RM) $@ $(CC) -o 3dANOVA2 3dANOVA2.o $(LFLAGS) $(LLIBS)3dANOVA3:3dANOVA3.o $(RM) $@ $(CC) -o 3dANOVA3 3dANOVA3.o $(LFLAGS) $(LLIBS)3dNLfim:3dNLfim.o NLfit.c NLfit.h NLfit_model.c NLfit_model.h simplex.c parser.o parser_int.o $(RM) $@ $(CCFAST) -o 3dNLfim 3dNLfim.o $(PLFLAGS) $(LFLAGS) parser.o parser_int.o $(LLIBS)3dNLfim_n:3dNLfim_n.o NLfit.c NLfit.h NLfit_model.c NLfit_model.h simplex.c $(RM) $@ $(CC) -o 3dNLfim_n 3dNLfim_n.o $(PLFLAGS) $(LFLAGS) $(LLIBS)3dNeocon:3dNeocon.o $(RM) $@ $(CCFAST) -o 3dNeocon 3dNeocon.o $(PLFLAGS) $(LFLAGS) $(LLIBS)3dStatClust:3dStatClust.o $(RM) $@ $(CC) -o 3dStatClust 3dStatClust.o $(PLFLAGS) $(LLIBS)RSFgen:RSFgen.o $(RM) $@ $(CC) -o RSFgen RSFgen.o $(LFLAGS) $(LLIBS)3dTSgen:3dTSgen.o NLfit.c NLfit.h NLfit_model.c NLfit_model.h $(RM) $@ $(CC) -o 3dTSgen 3dTSgen.o $(PLFLAGS) $(LLIBS)3dFWHM:3dFWHM.o $(RM) $@ $(CC) -o 3dFWHM 3dFWHM.o $(LFLAGS) $(LLIBS)3dFWHMx:3dFWHMx.o $(RM) $@ $(CC) -o 3dFWHMx 3dFWHMx.o $(LFLAGS) $(LLIBS)3dMannWhitney:3dMannWhitney.o $(RM) $@ $(CC) -o 3dMannWhitney 3dMannWhitney.o $(LFLAGS) $(LLIBS)3dWilcoxon:3dWilcoxon.o $(RM) $@ $(CC) -o 3dWilcoxon 3dWilcoxon.o $(LFLAGS) $(LLIBS)3dWavelets:3dWavelets.o $(RM) $@ $(CC) -o 3dWavelets 3dWavelets.o $(LFLAGS) $(LLIBS)3dfim+:3dfim+.o $(RM) $@ $(CC) -o 3dfim+ 3dfim+.o $(LFLAGS) $(LLIBS)3dKruskalWallis:3dKruskalWallis.o $(RM) $@ $(CC) -o 3dKruskalWallis 3dKruskalWallis.o $(LFLAGS) $(LLIBS)3dFriedman:3dFriedman.o $(RM) $@ $(CC) -o 3dFriedman 3dFriedman.o $(LFLAGS) $(LLIBS)3dRegAna:3dRegAna.o $(RM) $@ $(CC) -o 3dRegAna 3dRegAna.o $(LFLAGS) $(LLIBS)# double precision version of 3dDeconvolve3dDeconvolve:3dDeconvolve.c Deconvolve.c RegAna.c matrix.c matrix.h parser.o parser_int.o $(RM) $@ $(CCFAST) -o 3dDeconvolve 3dDeconvolve.c parser.o parser_int.o $(INFLAGS) $(LFLAGS) -lcoxplot $(LLIBS)# float version of 3dDeconvolve3dDeconvolve_f:3dDeconvolve.c Deconvolve.c RegAna.c matrix_f.c matrix_f.h parser.o parser_int.o $(RM) $@ $(CCFAST) $(SPECIAL) -DFLOATIZE -o 3dDeconvolve_f 3dDeconvolve.c matrix_f.c parser.o parser_int.o $(INFLAGS) $(LFLAGS) -lcoxplot $(LLIBS)# double precision version of 3dDeconvolve3dDeconvolve_n:3dDeconvolve.c Deconvolve.c RegAna.c matrix.c matrix.h parser.o parser_int.o $(RM) $@ $(CC) -o 3dDeconvolve_n 3dDeconvolve.c parser.o parser_int.o $(INFLAGS) $(LFLAGS) -lcoxplot $(LLIBS)3dConvolve:3dConvolve.o $(RM) $@ $(CC) -o 3dConvolve 3dConvolve.o $(LFLAGS) $(LLIBS)3dIntracranial:3dIntracranial.o $(RM) $@ $(CC) -o 3dIntracranial 3dIntracranial.o $(LFLAGS) $(LLIBS)3dExtrema:3dExtrema.o $(RM) $@ $(CC) -o 3dExtrema 3dExtrema.o $(LFLAGS) $(LLIBS)adwarp:adwarp.o $(RM) $@ $(CC) -o adwarp adwarp.o $(LFLAGS) $(LLIBS)2dImReg:2dImReg.o $(RM) $@ $(CC) -o 2dImReg 2dImReg.o $(LFLAGS) $(LLIBS)waver:waver.o parser.o parser_int.o $(RM) $@ $(CC) -o waver waver.o parser.o parser_int.o $(LFLAGS) $(LLIBS)3dSimARMA11:3dSimARMA11.o $(RM) $@ $(CC) -o 3dSimARMA11 3dSimARMA11.o $(LFLAGS) $(LLIBS)3dnewid:3dnewid.o $(RM) $@ $(CC) -o 3dnewid 3dnewid.o $(LFLAGS) $(LLIBS)DTIStudioFibertoSegments:DTIStudioFibertoSegments.o $(RM) $@ $(CC) -o DTIStudioFibertoSegments DTIStudioFibertoSegments.o $(LFLAGS) $(LLIBS)mri_nstats.o:mri_nstats.c $(RM) $@ $(CCFAST) -c mri_nstats.c $(INFLAGS)3dLocalSVD.o:3dLocalSVD.c $(RM) $@ $(CC) -c 3dLocalSVD.c $(INFLAGS)3dLocalSVD:3dLocalSVD.o $(RM) $@ $(CC) -o 3dLocalSVD 3dLocalSVD.o $(LFLAGS) $(LLIBS)## ------- Things to be compiled or linked with OpenMP -------3dDimRed.o: 3dDimRed.c $(RM) $@ $(CCOMP) -c 3dDimRed.c $(INFLAGS)3dDimRed:3dDimRed.o $(RM) $@ $(CCOMP) -o 3dDimRed 3dDimRed.o $(LFLAGS) $(LLIBS)3dSatCheck.o: 3dSatCheck.c thd_satcheck.c $(RM) $@ $(CCOMP) -c 3dSatCheck.c $(INFLAGS)3dSatCheck:3dSatCheck.o $(RM) $@ $(CCOMP) -o 3dSatCheck 3dSatCheck.o $(LFLAGS) $(LLIBS)3dREMLfit.o: 3dREMLfit.c remla.c matrix.c rcmat.c $(RM) $@ $(CCOMP) -c 3dREMLfit.c $(INFLAGS)3dREMLfit:3dREMLfit.o $(RM) $@ $(CCOMP) -o 3dREMLfit 3dREMLfit.o $(LFLAGS) $(LLIBS)3dBandpass.o: 3dBandpass.c mri_blur3d_variable.c $(RM) $@ $(CCOMP) -c 3dBandpass.c $(INFLAGS)3dBandpass:3dBandpass.o $(RM) $@ $(CCOMP) -o 3dBandpass 3dBandpass.o $(LFLAGS) $(LLIBS)3dGroupInCorr.o:3dGroupInCorr.c $(RM) $@ $(CCOMP) -c 3dGroupInCorr.c $(INFLAGS)3dGroupInCorr:3dGroupInCorr.o $(RM) $@ $(CCOMP) -o 3dGroupInCorr 3dGroupInCorr.o $(LFLAGS) $(LLIBS)3dLocalPV.o:3dLocalPV.c cs_pv.c $(RM) $@ $(CCOMP) -c 3dLocalPV.c $(INFLAGS)3dLocalPV:3dLocalPV.o $(RM) $@ $(CCOMP) -o 3dLocalPV 3dLocalPV.o $(LFLAGS) $(LLIBS)3dLocalstat.o:3dLocalstat.c mri_nstats.c $(RM) $@ $(CCOMP) -c 3dLocalstat.c $(INFLAGS)3dLocalstat:3dLocalstat.o $(RM) $@ $(CCOMP) -o 3dLocalstat 3dLocalstat.o $(LFLAGS) $(LLIBS)AlphaSim.o:AlphaSim.c zgaussian.c $(RM) $@ $(CCOMP) -c AlphaSim.c $(INFLAGS)AlphaSim:AlphaSim.o $(RM) $@ $(CCOMP) -o AlphaSim AlphaSim.o $(LFLAGS) $(LLIBS)3dClustSim.o:3dClustSim.c zgaussian.c $(RM) $@ $(CCOMP) -c 3dClustSim.c $(INFLAGS)3dClustSim:3dClustSim.o $(RM) $@ $(CCOMP) -o 3dClustSim 3dClustSim.o $(LFLAGS) $(LLIBS)3dBlurInMask.o:3dBlurInMask.c $(RM) $@ $(CCOMP) -c 3dBlurInMask.c $(INFLAGS)3dTcorrMap:3dTcorrMap.o $(RM) $@ $(CCOMP) -o 3dTcorrMap 3dTcorrMap.o $(LFLAGS) $(LLIBS)3dTmatch:3dTmatch.o $(RM) $@ $(CCOMP) -o 3dTmatch 3dTmatch.o $(LFLAGS) $(LLIBS)3dTcorr1D:3dTcorr1D.o $(RM) $@ $(CCOMP) -o 3dTcorr1D 3dTcorr1D.o $(LFLAGS) $(LLIBS)3dBlurInMask:3dBlurInMask.o $(RM) $@ $(CCOMP) -o 3dBlurInMask 3dBlurInMask.o $(LFLAGS) $(LLIBS)3dDespike.o:3dDespike.c $(RM) $@ $(CCOMP) -c 3dDespike.c $(INFLAGS)3dDespike:3dDespike.o $(RM) $@ $(CCOMP) -o 3dDespike 3dDespike.o $(LFLAGS) $(LLIBS)3dAllineate:3dAllineate.o mri_genalign.c mri_genalign_util.c thd_correlate.c $(RM) $@ $(CCOMP) -o 3dAllineate 3dAllineate.o $(LFLAGS) $(LLIBS)3dQwarp:3dQwarp.o mri_genalign.c mri_genalign_util.c mri_nwarp.c thd_incorrelate.c $(RM) $@ $(CCOMP) -o 3dQwarp 3dQwarp.o $(LFLAGS) $(LLIBS)3dQwarp.o:3dQwarp.c mri_genalign.c mri_genalign_util.c thd_incorrelate.c mri_nwarp.c $(RM) $@ $(CCOMP) -c 3dQwarp.c $(INFLAGS)3dNwarpApply:3dNwarpApply.o $(RM) $@ $(CCOMP) -o 3dNwarpApply 3dNwarpApply.o $(LFLAGS) $(LLIBS)3dNwarpCalc:3dNwarpCalc.o $(RM) $@ $(CCOMP) -o 3dNwarpCalc 3dNwarpCalc.o $(LFLAGS) $(LLIBS)3dRBFdset:3dRBFdset.o mri_rbfinterp.o $(RM) $@ $(CCOMP) -o 3dRBFdset 3dRBFdset.o $(LFLAGS) $(LLIBS)3dAutoTcorrelate.o:3dAutoTcorrelate.c $(RM) $@ $(CCOMP) -c 3dAutoTcorrelate.c $(INFLAGS)3dAutoTcorrelate:3dAutoTcorrelate.o $(RM) $@ $(CCOMP) -o 3dAutoTcorrelate 3dAutoTcorrelate.o $(LFLAGS) $(LLIBS)mri_rbfinterp.o:mri_rbfinterp.c $(RM) $@ $(CCOMP) -c mri_rbfinterp.c $(INFLAGS)3dAllineate.o:3dAllineate.c mri_genalign.c mri_genalign_util.c thd_correlate.c $(RM) $@ $(CCOMP) -c 3dAllineate.c $(INFLAGS)3dNwarpApply.o:3dNwarpApply.c mri_nwarp.c $(RM) $@ $(CCOMP) -c 3dNwarpApply.c $(INFLAGS)3dNwarpCalc.o:3dNwarpCalc.c mri_nwarp.c $(RM) $@ $(CCOMP) -c 3dNwarpCalc.c $(INFLAGS)3dTcorrMap.o:3dTcorrMap.c $(RM) $@ $(CCOMP) -c 3dTcorrMap.c $(INFLAGS)3dTmatch.o:3dTmatch.c $(RM) $@ $(CCOMP) -c 3dTmatch.c $(INFLAGS)3dTcorr1D.o:3dTcorr1D.c $(RM) $@ $(CCOMP) -c 3dTcorr1D.c $(INFLAGS)## ------- end of OpenMP compilations -------# in case I want to CCOMP this somedaymcw_malloc.o:mcw_malloc.c $(RM) $@ $(CC) -c mcw_malloc.c $(INFLAGS)### generic compile a C file.c.o: $(RM) $@ $(CC) -c $*.c $(INFLAGS)### Special compilations for the reslicing routines, which### are templates that require definition of the data type### upon which they operate.afni_slice_short.o:3ddata.h afni_slice.c afni_warp.h $(RM) $@ $(CC) -c -DDTYPE=short afni_slice.c $(INFLAGS) $(MV) afni_slice.o afni_slice_short.oafni_slice_float.o:3ddata.h afni_slice.c afni_warp.h $(RM) $@ $(CC) -c -DDTYPE=float afni_slice.c $(INFLAGS) $(MV) afni_slice.o afni_slice_float.oafni_slice_byte.o:3ddata.h afni_slice.c afni_warp.h $(RM) $@ $(CC) -c -DDTYPE=byte afni_slice.c $(INFLAGS) $(MV) afni_slice.o afni_slice_byte.oafni_slice_int.o:3ddata.h afni_slice.c afni_warp.h $(RM) $@ $(CC) -c -DDTYPE=int afni_slice.c $(INFLAGS) $(MV) afni_slice.o afni_slice_int.oafni_slice_complex.o:3ddata.h afni_slice.c afni_warp.h $(RM) $@ $(CC) -c -DDTYPE=complex afni_slice.c $(INFLAGS) $(MV) afni_slice.o afni_slice_complex.oafni_slice_rgbyte.o:3ddata.h afni_slice.c afni_warp.h $(RM) $@ $(CC) -c -DDTYPE=rgbyte afni_slice.c $(INFLAGS) $(MV) afni_slice.o afni_slice_rgbyte.oafni_slice_rgba.o:3ddata.h afni_slice.c afni_warp.h $(RM) $@ $(CC) -c -DDTYPE=rgba afni_slice.c $(INFLAGS) $(MV) afni_slice.o afni_slice_rgba.oafni_pcor_byte.o:afni_pcor.h afni_pcor_update.c $(RM) $@ $(CC) -c -DDTYPE=byte afni_pcor_update.c $(INFLAGS) $(MV) afni_pcor_update.o afni_pcor_byte.oafni_pcor_float.o:afni_pcor.h afni_pcor_update.c $(RM) $@ $(CC) -c -DDTYPE=float afni_pcor_update.c $(INFLAGS) $(MV) afni_pcor_update.o afni_pcor_float.oafni_pcor_short.o:afni_pcor.h afni_pcor_update.c $(RM) $@ $(CC) -c -DDTYPE=short afni_pcor_update.c $(INFLAGS) $(MV) afni_pcor_update.o afni_pcor_short.o### End of reslicing routines# SHOWOFF = -DSHOWOFF=NO### The star of the showafni.o:afni.c niml.h $(RM) $@ $(CC) -c afni.c $(INFLAGS) $(SHOWOFF)afni_version.o:afni_version.c $(RM) $@ $(CC) -c afni_version.c $(INFLAGS) $(SHOWOFF)afni:$(AFOBJS) libcoxplot.a libmri.a libmrix.a libvolpack.a libjpeg.a libXmHTML.a volpack.h coxplot.h niml.h $(RM) $@ $(CC) -o afni $(AFOBJS) $(PLFLAGS) -lmrix -lcoxplot -lmri -lvolpack libXmHTML.a libjpeg.a $(LLIBS) -lm -lcafni+:$(AFOBJS) libcoxplot.a libmri.a libmrix.a coxplot.h niml.h $(RM) $@ $(CC) -o afni+ $(AFOBJS) $(PLFLAGS) -lmrix -lcoxplot $(LLIBS) -lm -lcmotiftoy: afni motiftoy.c $(RM) $@ $(CC) -o motiftoy motiftoy.c $(INFLAGS) $(SHOWOFF) $(PLFLAGS) -lmrix -lcoxplot -lmri -lvolpack $(LLIBS) -lm -lc# CYGWIN: must compile afni.exe with fixed plugins (see PLUGIN_FIXED, far below)afni.exe:$(AFOBJS) plugin_fixed libcoxplot.a libvolpack.a libmri.a libmrix.a volpack.h coxplot.h niml.h $(RM) $@ $(CC) -o afni $(AFOBJS) $(PLUGIN_FIXED) $(LFLAGS) -lmrix -lcoxplot -lmri -lvolpack $(LLIBS)### If you have Purify# pafni:$(AFOBJS) libcoxplot.a# $(RM) $@# purify $(CC) -o pafni $(AFOBJS) $(PLFLAGS) -lcoxplot $(LLIBS)### This program is only used with XFree86 4.0 and abovexiner:xiner.o $(RM) $@ $(CC) -o xiner xiner.o $(LFLAGS) -lXinerama $(LLIBS)cat_matvec:cat_matvec.o $(RM) $@ $(CC) -o cat_matvec cat_matvec.o $(LFLAGS) $(LLIBS)to3d:to3d.h $(T3OBJS) libcoxplot.a $(RM) $@ $(CC) -o to3d $(T3OBJS) $(LFLAGS) -lmrix -lcoxplot $(LLIBS)1dplot:libcoxplot.a 1dplot.o display.o $(RM) $@ $(CC) -o 1dplot 1dplot.o display.o $(LFLAGS) -lcoxplot -lmrix $(LLIBS)1dgrayplot:libcoxplot.a 1dgrayplot.o display.o $(RM) $@ $(CC) -o 1dgrayplot 1dgrayplot.o display.o $(LFLAGS) -lcoxplot $(LLIBS)1dsigplot:libcoxplot.a 1dsigplot.o display.o $(RM) $@ $(CC) -o 1dsigplot 1dsigplot.o display.o $(LFLAGS) -lcoxplot $(LLIBS)1dtranspose:1dtranspose.o $(RM) $@ $(CC) -o 1dtranspose 1dtranspose.o $(LFLAGS) $(LLIBS)1dREMLfit.o: 1dREMLfit.c remla.c1dREMLfit:1dREMLfit.o $(RM) $@ $(CC) -o 1dREMLfit 1dREMLfit.o $(LFLAGS) $(LLIBS)mri_blur3d_variable.o:mri_blur3d_variable.c $(RM) $@ $(CCFAST) -c mri_blur3d_variable.c $(INFLAGS)1dUpsample:1dUpsample.o $(RM) $@ $(CC) -o 1dUpsample 1dUpsample.o $(LFLAGS) $(LLIBS)3dUpsample:3dUpsample.o $(RM) $@ $(CC) -o 3dUpsample 3dUpsample.o $(LFLAGS) $(LLIBS)1dTsort:1dTsort.o $(RM) $@ $(CC) -o 1dTsort 1dTsort.o $(LFLAGS) $(LLIBS)1dGentimes:1dGentimes.o $(RM) $@ $(CC) -o 1dGentimes 1dGentimes.o $(LFLAGS) $(LLIBS)1dRansplit:1dRansplit.o $(RM) $@ $(CC) -o 1dRansplit 1dRansplit.o $(LFLAGS) $(LLIBS)afni_vcheck:afni_vcheck.o $(RM) $@ $(CC) -o afni_vcheck afni_vcheck.o $(LFLAGS) $(LLIBS)1dfft:1dfft.o $(RM) $@ $(CC) -o 1dfft 1dfft.o $(LFLAGS) $(LLIBS)1dgenARMA11:1dgenARMA11.o $(RM) $@ $(CC) -o 1dgenARMA11 1dgenARMA11.o $(LFLAGS) $(LLIBS)1dBandpass:1dBandpass.o $(RM) $@ $(CC) -o 1dBandpass 1dBandpass.o $(LFLAGS) $(LLIBS)1dcat:1dcat.o $(RM) $@ $(CC) -o 1dcat 1dcat.o $(LFLAGS) $(LLIBS)2perm:2perm.o $(CC) -o 2perm 2perm.o $(INFLAGS) $(LFLAGS) $(LLIBS)3dClustCount:3dClustCount.o $(RM) $@ $(CC) -o 3dClustCount 3dClustCount.o $(LFLAGS) $(LLIBS)1dMarry:1dMarry.o $(RM) $@ $(CC) -o 1dMarry 1dMarry.o $(LFLAGS) $(LLIBS)3dEmpty:3dEmpty.o $(RM) $@ $(CC) -o 3dEmpty 3dEmpty.o $(LFLAGS) $(LLIBS)1ddot:1ddot.o $(RM) $@ $(CC) -o 1ddot 1ddot.o $(LFLAGS) $(LLIBS)qtest:thd_bstrap_corr.o $(RM) $@ $(CC) -o qtest thd_bstrap_corr.o $(LFLAGS) $(LLIBS)1dcorr:1dcorr.o $(RM) $@ $(CC) -o 1dcorr 1dcorr.o $(LFLAGS) $(LLIBS)1dCorrelate:1dCorrelate.o $(RM) $@ $(CC) -o 1dCorrelate 1dCorrelate.o $(LFLAGS) $(LLIBS)1dsvd:1dsvd.o $(RM) $@ $(CC) -o 1dsvd 1dsvd.o $(LFLAGS) $(LLIBS)1dsum:1dsum.o $(RM) $@ $(CC) -o 1dsum 1dsum.o $(LFLAGS) $(LLIBS)1dnorm:1dnorm.o $(RM) $@ $(CC) -o 1dnorm 1dnorm.o $(LFLAGS) $(LLIBS)1dFlagMotion:1dFlagMotion.o $(RM) $@ $(CC) -o 1dFlagMotion 1dFlagMotion.o $(LFLAGS) $(LLIBS)abut:abut.o $(RM) $@ $(CC) -o abut abut.o $(LFLAGS) $(LLIBS)siemens_vision:siemens_vision.o $(RM) $@ $(CC) -o siemens_vision siemens_vision.o $(LFLAGS) $(LLIBS)ge_header:ge_header.o $(RM) $@ $(CC) -o ge_header ge_header.o $(LFLAGS) $(LLIBS)mayo_analyze:mayo_analyze.o $(RM) $@ $(CC) -o mayo_analyze mayo_analyze.o $(LFLAGS) $(LLIBS)dicom_hdr:dicom_hdr.o $(RM) $@ $(CC) -o dicom_hdr dicom_hdr.o $(LFLAGS) $(LLIBS)dicom_hinfo:dicom_hinfo.o $(RM) $@ $(CC) -o dicom_hinfo dicom_hinfo.o $(LFLAGS) $(LLIBS)dicom_to_raw:dicom_to_raw.o $(RM) $@ $(CC) -o dicom_to_raw dicom_to_raw.o $(LFLAGS) $(LLIBS)sfim:sfim.o $(RM) $@ $(CC) -o sfim sfim.o $(LFLAGS) $(LLIBS)tfim:tfim.o $(RM) $@ $(CC) -o tfim tfim.o $(LFLAGS) $(LLIBS)ftosh:ftosh.o $(RM) $@ $(CC) -o ftosh ftosh.o $(LFLAGS) $(LLIBS)ppmtoargb:ppmtoargb.o $(RM) $@ $(CC) -o ppmtoargb ppmtoargb.o $(LFLAGS) $(LLIBS)colari:colari.o $(RM) $@ $(CC) -o colari colari.o $(LFLAGS) $(LLIBS)iotest:iotest.o $(RM) $@ $(CC) -o iotest iotest.o $(LFLAGS) $(LLIBS)iochan_relay:iochan_relay.o $(RM) $@ $(CC) -o iochan_relay iochan_relay.o $(LFLAGS) $(LLIBS)3dFFT:3dFFT.o $(RM) $@ $(CCFAST) -o 3dFFT 3dFFT.o $(LFLAGS) $(LLIBS)3dLSS.o:3dLSS.c $(RM) $@ $(CCFAST) -c 3dLSS.c $(INFLAGS)3dLSS:3dLSS.o $(RM) $@ $(CCFAST) -o 3dLSS 3dLSS.o $(LFLAGS) $(LLIBS)### These programs are from Tom Ross3dFourier:3dFourier.o $(RM) $@ $(CC) -o 3dFourier 3dFourier.o $(LFLAGS) $(LLIBS)3dNotes:3dNotes.o $(RM) $@ $(CC) -o 3dNotes 3dNotes.o $(LFLAGS) $(LLIBS)3dROIstats:3dROIstats.o $(RM) $@ $(CC) -o 3dROIstats 3dROIstats.o $(LFLAGS) $(LLIBS)3dCM:3dCM.o $(RM) $@ $(CC) -o 3dCM 3dCM.o $(LFLAGS) $(LLIBS)3dSpatNorm:3dSpatNorm.o $(RM) $@ $(CC) -o 3dSpatNorm 3dSpatNorm.o $(LFLAGS) $(LLIBS)### These programs are from Fred Tam3dretroicor:3dretroicor.o retroicor.o $(RM) $@ $(CC) -o 3dretroicor 3dretroicor.o retroicor.o $(LFLAGS) $(LLIBS)### These programs are from Matthew Belmonteballoon:balloon.o $(RM) $@ $(CC) -o balloon balloon.o $(LFLAGS) -lgsl -lgslcblas -lm### Test area for surface datasets Placed here by ZSS for RickRsuma_datasets.o: suma_datasets.c $(RM) $@ $(CC) -c suma_datasets.c -o $@ -ISUMA/ $(INFLAGS)suma_algorithms.o: suma_algorithms.c $(RM) $@ $(CC) -c suma_algorithms.c -o $@ -ISUMA/ $(INFLAGS)testdsetio: SUMA/SUMA_TestDsetIO.c suma_datasets.o suma_algorithms.o $(RM) $@ $(CC) -o testdsetio SUMA/SUMA_TestDsetIO.c suma_datasets.o suma_algorithms.o \ -ISUMA/ $(INFLAGS) $(LFLAGS) $(LLIBS)### Sort of cleanclean: $(RM) `find . -name \*.o -print`cleann: $(RM) `find . -name \*.o -print`cleaner:clean $(RM) *.a $(PROGRAMS)cleanest: $(RM) `find . -name \*.o -print` $(RM) `find . -name \*.so -print` $(RM) `find . -name \*.a -print` $(RM) $(PROGRAMS) $(RM) SUMA/SUMA_*.tarclean_progs: $(RM) $(PROGRAMS)# CYGWIN: remove the fixed plugins as wellclean_exe: $(RM) *.o *.fixed#backup:# ssh afni chmod -R u+w /home/rwcox/AFNI_BACKUP# scp -prq * afni:/home/rwcox/AFNI_BACKUPbackup: chmod -R u+w /net/afni/home2/AFNI/BACKUP/ cp -pr * /net/afni/home2/AFNI/BACKUP### Make the source distributionafni_src.tgz: $(MKDIR) afni_src $(CP) -p *.c *.f *.inc *.h *.hhh Makefile.* *.xbm $(MINDOCS) $(MISC) ./afni_src $(CP) -pr coxplot volpack moveup moveAFNI* eispack avovk ptaylor pkundu ./afni_src $(CP) -pr $(SCRIPTS) $(PY_DIR) $(R_DIR) ./afni_src $(CP) -pr gifsicledir qhulldir f2cdir mpeg_encodedir ./afni_src $(CP) -pr 3DEdge netcdf-3.5.0 jpeg-6b niml Makefile_* nifti dlcompat ./afni_src $(CP) -pr SUMA svm matlab rickr faces poems gifti ni_test_? README.* ./afni_src $(CP) -pr XmHTML html ./afni_src chmod -R ugo+rw ./afni_src $(TAR) cf - afni_src | $(GZIP) -9v > afni_src.tgz $(RM) -r ./afni_src# in above list# mpegtoppm_dir ./afni_src### Make the source of the Matlab codeafni_matlab.tgz: $(MKDIR) afni_matlab $(CP) -pr matlab ./afni_matlab chmod ugo+rwx ./afni_matlab/* $(TAR) cf - afni_matlab | $(GZIP) -9v > afni_matlab.tgz $(RM) -r afni_matlab### Make the documentation distribution: only for use by RWCoxafni_doc.tgz: $(RM) $@ $(MKDIR) ./afni_doc $(CP) $(DOCS) ./afni_doc $(TAR) cf - ./afni_doc | $(GZIP) -9v > afni_doc.tgz $(RM) -r ./afni_doc### Put things in their placesinstall: $(INSTALLDIR) $(INSTALL_PREREQ) ptaylor_install pkundu_install $(MV) $(PROGRAMS) $(INSTALLDIR) $(CP) $(SCRIPTS) $(INSTALLDIR) $(CP) $(PY_DIR)/*.py $(R_DIR)/*.R $(INSTALLDIR) $(CP) html/??*.* $(EXTRA_INSTALL_FILES) $(INSTALLDIR) if [ -f README.environment ]; then $(CP) README.* $(INSTALLDIR); fi; if [ -f AFNI.afnirc ]; then $(CP) AFNI.afnirc $(INSTALLDIR); fi; if [ -f AFNI.sumarc ]; then $(CP) AFNI.sumarc $(INSTALLDIR); fi; if [ -f R_io.so ]; then $(CP) R_io.so $(INSTALLDIR); fi; if [ -f AFNI_atlas_spaces.niml ]; then $(CP) AFNI_atlas_spaces.niml $(INSTALLDIR); fi; $(EXINCOM) echo "===== AFNI install finished (fondly do we hope, fervently we do pray) ====="install_noplug: $(INSTALLDIR) $(MV) $(PROGRAMS_NOPLUG) $(INSTALLDIR) $(CP) $(SCRIPTS) $(INSTALLDIR) $(CP) $(PY_DIR)/*.py $(R_DIR)/*.R $(INSTALLDIR)install_lib: $(LIBDIR) $(CP) libmri.a libmrix.a libf2c.a libcoxplot.a libvolpack.a $(LIBHEADERS) $(LIBDIR)# CYGWIN: must put the .exe suffix on the "mv" command for some reasoninstall_exe: $(INSTALLDIR) ( for pp in $(PROGRAMS_EXE) ; do \ qq=`basename $$pp .exe`; $(MV) $${qq}.exe $(INSTALLDIR) ; \ done ) $(CP) $(SCRIPTS) $(INSTALLDIR) $(CP) $(PY_DIR)/*.py $(R_DIR)/*.R $(INSTALLDIR)#################################################################### some dependencies (not complete)afni.o:imseq.h 3ddata.h xutil.h pbar.h afni.h bbox.h afni_warp.h \ afni_graph.h afni_setup.h machdep.hdebugtrace.o:debugtrace.h debugtrace.c $(RM) $@ $(CC) -c debugtrace.c $(INFLAGS) $(SHOWOFF)afni_vcheck.o:afni.hafni_splash.o:afni_splash.h imseq.h afni_splash.cafni_func.o:imseq.h 3ddata.h xutil.h pbar.h afni.h machdep.hafni_widg.o:imseq.h 3ddata.h xutil.h pbar.h afni.h logo.h machdep.hafni_warp.o:afni_warp.h 3ddata.h machdep.hafni_graph.o:afni_graph.h 3ddata.h xutil.h bbox.h afni.h machdep.hafni_fimmer.o:afni_graph.h afni.h machdep.hafni_plugin.o:afni_plugin.h 3ddata.h xutil.h afni.h bbox.h afni_warp.h \ machdep.h display.h imseq.hafni_plugout.o:afni_plugin.h afni_plugout.h machdep.hafni_setup.o:afni.h afni_setup.h pbar.h3dclust.o:3ddata.h3dmerge.o:3ddata.hpbar.o:pbar.h machdep.hbbox.o:bbox.h xutil.h coxplot.hxutil.o:xutil.himseq.o:imseq.h display.h bbox.h xutil.h mrilib.hdisplay.o:display.h mrilib.hxim.o:xim.h display.h mrilib.hts.o:ts.hto3d.o:to3d.h3dbucket.o:3ddata.h3dTSgen.o:NLfit.c NLfit.h NLfit_model.c NLfit_model.hmcw_graf.o:mcw_graf.h#################################################################### make the mri libraryafni_suma.o:afni_suma.c afni_suma.h cs_sort_template.h $(RM) $@ $(CCFAST) -c afni_suma.c $(INFLAGS)csfft.o:csfft.c $(RM) $@ $(CCFAST) -c csfft.c $(INFLAGS)mri_percents.o:mri_percents.c $(RM) $@ $(CCFAST) -c mri_percents.c $(INFLAGS)mri_warpfield.o:mri_warpfield.c $(RM) $@ $(CCFAST) -c mri_warpfield.c $(INFLAGS)edt_clustalpha.o:AlphaTab64.h edt_clustalpha.c $(RM) $@ $(CCFAST) -c edt_clustalpha.c $(INFLAGS)afni_pplug_instacorr.o:afni_pplug_instacorr.c $(RM) $@ $(CCFAST) -c afni_pplug_instacorr.c $(INFLAGS)afni_pplug_instacalc.o:afni_pplug_instacalc.c $(RM) $@ $(CCFAST) -c afni_pplug_instacalc.c $(INFLAGS)mri_nbistats.o:mri_nbistats.c $(RM) $@ $(CCFAST) -c mri_nbistats.c $(INFLAGS)mri_to_float.o:mri_to_float.c $(RM) $@ $(CCFAST) -c mri_to_float.c $(INFLAGS)mri_to_short.o:mri_to_short.c $(RM) $@ $(CCFAST) -c mri_to_short.c $(INFLAGS)mri_to_byte.o:mri_to_byte.c $(RM) $@ $(CCFAST) -c mri_to_byte.c $(INFLAGS)cs_symeig.o:cs_symeig.c $(RM) $@ $(CCFAST) -c cs_symeig.c $(INFLAGS)cs_pv.o:cs_pv.c $(RM) $@ $(CCFAST) -c cs_pv.c $(INFLAGS)cs_qmed.o:cs_qmed.c $(RM) $@ $(CCFAST) -c cs_qmed.c $(INFLAGS)cs_sort_ff.o:cs_sort_ff.c $(RM) $@ $(CCFAST) -c cs_sort_ff.c $(INFLAGS)cs_sort_fi.o:cs_sort_fi.c $(RM) $@ $(CCFAST) -c cs_sort_fi.c $(INFLAGS)cs_sort_fv.o:cs_sort_fv.c $(RM) $@ $(CCFAST) -c cs_sort_fv.c $(INFLAGS)cs_sort_iv.o:cs_sort_iv.c $(RM) $@ $(CCFAST) -c cs_sort_iv.c $(INFLAGS)cs_sort_dv.o:cs_sort_dv.c $(RM) $@ $(CCFAST) -c cs_sort_dv.c $(INFLAGS)cs_sort_d.o:cs_sort_d.c $(RM) $@ $(CCFAST) -c cs_sort_d.c $(INFLAGS)3dNLfim.o:3dNLfim.c NLfit.c NLfit.h NLfit_model.c NLfit_model.h $(RM) $@ $(CCFAST) -c 3dNLfim.c $(INFLAGS)3dNLfim_n.o:3dNLfim.c NLfit.c NLfit.h NLfit_model.c NLfit_model.h $(RM) 3dNLfim.o 3dNLfim_n.o $(CC) -c 3dNLfim.c $(INFLAGS) $(MV) 3dNLfim.o 3dNLfim_n.opowell_newuoa.o:powell_newuoa.c $(RM) $@ $(CCFAST) -c powell_newuoa.c $(INFLAGS)mri_genalign_util.o:mri_genalign_util.c $(RM) $@ $(CCFAST) -c mri_genalign_util.c $(INFLAGS)mri_genalign.o:mri_genalign.c $(RM) $@ $(CCFAST) -c mri_genalign.c $(INFLAGS)thd_correlate.o:thd_correlate.c $(RM) $@ $(CCFAST) -c thd_correlate.c $(INFLAGS)thd_incorrelate.o:thd_incorrelate.c $(RM) $@ $(CCFAST) -c thd_incorrelate.c $(INFLAGS)cl1.o:cl1.c $(RM) $@ $(CCFAST) -c cl1.c $(INFLAGS)cl2.o:cl2.c $(RM) $@ $(CCFAST) -c cl2.c $(INFLAGS)mri_drawing.o:mri_drawing.c $(RM) $@ $(CCFAST) -c mri_drawing.c $(INFLAGS)mri_dup.o:mri_dup.c $(RM) $@ $(CCFAST) -c mri_dup.c $(INFLAGS)mri_warp.o:mri_warp.c $(RM) $@ $(CCFAST) -c mri_warp.c $(INFLAGS)mri_warp3D.o:mri_warp3D.c $(RM) $@ $(CCFAST) -c mri_warp3D.c $(INFLAGS)mri_warp3D_align.o:mri_warp3D_align.c $(RM) $@ $(CCFAST) -c mri_warp3D_align.c $(INFLAGS)thd_rot3d.o:thd_rot3d.c $(RM) $@ $(CCFAST) -c thd_rot3d.c $(INFLAGS)thd_automask.o:thd_automask.c $(RM) $@ $(CCFAST) -c thd_automask.c $(INFLAGS)# can't use CCFAST on thd_shift2 because GCC optimizer failsthd_shift2.o:thd_shift2.c $(RM) $@ $(CC) -c thd_shift2.c $(INFLAGS)thd_rot3d_byte.o:thd_rot3d_byte.c $(RM) $@ $(CCFAST) -c thd_rot3d_byte.c $(INFLAGS)thd_svdblur.o:thd_svdblur.c $(RM) $@ $(CCFAST) -c thd_svdblur.c $(INFLAGS)cox_render.o:cox_render.h cox_render.c $(RM) $@ $(CCFAST) -c cox_render.c $(INFLAGS)mri_matrix.o:mri_matrix.c $(RM) $@ $(CCFAST) -c mri_matrix.c $(INFLAGS)rcmat.o:rcmat.c $(RM) $@ $(CCFAST) -c rcmat.c $(INFLAGS)thd_fitter.o:thd_fitter.c $(RM) $@ $(CCFAST) -c thd_fitter.c $(INFLAGS)thd_lasso.o:thd_lasso.c $(RM) $@ $(CCFAST) -c thd_lasso.c $(INFLAGS)MRI_OBJS = mri_cfft.o mri_complex_arith.o mri_fft_complex.o mri_free.o \ mri_max.o mri_new.o mri_read.o mri_swapbytes.o mri_dup.o \ mri_to_byte.o mri_to_complex.o mri_to_float.o mri_to_short.o \ mri_warp.o mri_write.o mri_float_func.o mri_edit.o mri_stat_seq.o \ mri_add_name.o mri_histog.o mri_nsize.o mri_lsqfit.o mri_sobel.o \ csfft.o mri_filt_fft.o mri_align.o mri_rota.o mri_thresh.o \ mri_to_mri.o mri_flippo.o mri_percents.o mri_stats.o mri_cat2D.o \ mri_transpose.o mri_shifter.o mcw_glob.o mri_2dalign.o mri_order.o \ mri_3dalign.o mri_render.o mri_to_rgb.o mcw_malloc.o mri_cut.o \ mri_overlay.o mri_copy.o mri_uncat2D.o cox_render.o mri_histobyte.o \ mri_aff2d.o debugtrace.o mri_zeropad.o mri_write_angif.o \ mri_histoshort.o mri_shift2D.o mri_drawing.o mri_coxplot.o \ mri_get_cmass.o mri_scale.o mri_write_analyze.o mri_to_rgba.o \ mri_rgba_compose.o mri_blur3d.o mri_dicom_hdr.o mri_read_dicom.o \ mri_read_stuff.o mri_flip3D.o mri_warp3D.o mri_fromstring.o \ ge4_header.o mri_equal.o mri_scalize.o mri_isgray.o mri_read_mpeg.o \ mri_entropy16.o mri_symbolize.o mri_colorsetup.o mri_warp3D_align.o \ mri_medianfilter.o mri_nstats.o mri_scaled_diff.o mri_matrix.o \ mri_genalign.o mri_clusterize.o mri_nbistats.o mri_fwhm.o \ mri_blur3d_variable.o mri_purger.o mri_counter.o mri_to_imarr.o \ mri_pcvector.o mri_fdrize.o mri_floatvec.o mri_sort.o \ mri_warpfield.o mri_dicom_stuff.o mri_check.o mri_allzero.o \ mri_subset.o mri_to_fvect.o mri_genalign_util.o rcmat.o dmat44.o \ mri_rbfinterp.o mri_genARMA11.o mri_catvol.o mri_polyfit.o \ mri_nwarp.o mri_extract.oTHD_OBJS = thd_atr.o thd_dsetto1D.o thd_initalldir.o thd_reconpar.o \ thd_auxdata.o thd_editdaxes.o thd_initdblk.o thd_sarr.o \ thd_bstats.o thd_fdbrick.o thd_initdkptr.o thd_statpval.o \ thd_compress.o thd_fdto1D.o thd_initprefix.o thd_timeof.o \ thd_coords.o thd_fdto2D.o thd_initsess.o thd_warps.o \ thd_countb.o thd_filestuff.o thd_linecount.o thd_writeatr.o \ thd_delete.o thd_forcemalloc.o thd_loaddblk.o thd_writedblk.o \ thd_dsetdblk.o thd_get1D.o thd_manydset.o thd_writedset.o \ thd_dsetinsess.o thd_idcode.o thd_opendset.o thd_zblock.o \ thd_dsetinslist.o thd_info.o thd_purgedblk.o thd_http.o \ thd_iochan.o thd_makefbuc.o thd_makefim.o thd_makefith.o \ thd_trusthost.o thd_rot3d.o thd_mastery.o thd_intlist.o \ thd_checkidc.o thd_floatscan.o thd_notes.o thd_makemask.o \ thd_shift2.o thd_1Dtodset.o thd_detrend.o thd_fitter.o \ thd_winsor.o thd_zeropad.o thd_rot3d_byte.o thd_shear3d.o \ thd_tmask.o thd_rotangles.o thd_ttest.o thd_center.o \ thd_mismatch.o thd_read_vecmat.o thd_tshift.o thd_newprefix.o \ thd_entropy16.o thd_dsetrow.o thd_rowfillin.o thd_fetchdset.o \ thd_getpathprogs.o thd_zfillin.o thd_ttatlas_query.o \ thd_dsetto3D.o thd_median.o thd_cliplevel.o thd_automask.o \ thd_outlier_count.o thd_correlate.o thd_autonudge.o thd_avts.o \ thd_mincwrite.o thd_mnicoords.o thd_strfunc.o thd_niftiwrite.o \ thd_analyzeread.o thd_ctfread.o thd_1Ddset.o thd_getorient.o \ thd_3Ddset.o thd_mattor.o thd_niftiread.o thd_mpegread.o \ thd_brainormalize.o thd_opentcat.o thd_nimlatr.o thd_dsetatr.o \ thd_logafni.o thd_dset_nbhd.o thd_vcheck.o thd_matdaxes.o \ thd_niml.o afni_vedit.o thd_fdrcurve.o thd_dset_to_vectim.o \ thd_bandpass.o thd_instacorr.o thd_svdblur.o thd_satcheck.o \ thd_dumdset.o ktaub.o bilinear_warp3D.o thd_table.o \ thd_atlas.o thd_warp_tables.o thd_lasso.o# these are now included in NIMLUNUSED_OBSJ = thd_md5.o thd_base64.oNIML_OBJS = niml_b64.o niml_element.o niml_elemio.o niml_registry.o \ niml_util.o niml_byteorder.o niml_header.o niml_malloc.o \ niml_rowtype.o niml_uuid.o niml_do.o niml_htable.o \ niml_md5.o niml_url.o niml_stream.o niml_struct.o \ niml_dataset.o niml_vector.o niml_stat.o niml_dtable.o \ niml_sucker.oEDT_OBJS = edt_addbrick.o edt_blur.o edt_buildmask.o edt_checkargv.o \ edt_clust.o edt_clustarr.o edt_coerce.o edt_dsetitems.o \ edt_emptycopy.o edt_filtervol.o edt_help.o edt_onedset.o \ edt_scl2max.o edt_substbrick.o edt_volamax.o edt_zscore.o \ edt_fullcopy.o edt_calcmask.o edt_volpad.o edt_sortmask.o \ edt_clust2.o edt_wodcopy.o edt_clustalpha.o edt_geomcon.o \ edt_floatize.oCS_OBJS = cs_sort_fi.o cs_sort_di.o cs_symeig.o cs_sort_ii.o cs_sort_ff.o \ cs_addto_args.o multivector.o afni_environ.o cs_qmed.o cl2.o \ cs_sort_fv.o cs_laguerre.o machdep.o cs_qhull.o afni_logger.o \ cl1.o cs_misc.o powell_int.o powell_newuoa.o cs_sort_dv.o \ rhdd.o zfun.o cs_pv.o cs_sort_iv.o cs_sort_d.o cs_fgets.oEIS_OBJS = eis_bakvec.o eis_balanc.o eis_balbak.o eis_bandr.o \ eis_bandv.o eis_bisect.o eis_bqr.o eis_cbabk2.o eis_cbal.o \ eis_cdiv.o eis_cg.o eis_ch.o eis_cinvit.o eis_combak.o \ eis_comhes.o eis_comlr.o eis_comlr2.o eis_comqr.o eis_comqr2.o \ eis_cortb.o eis_corth.o eis_csroot.o eis_elmbak.o eis_elmhes.o \ eis_eltran.o eis_epslon.o eis_figi.o eis_figi2.o eis_hqr.o \ eis_hqr2.o eis_htrib3.o eis_htribk.o eis_htrid3.o eis_htridi.o \ eis_imtql1.o eis_imtql2.o eis_imtqlv.o eis_invit.o eis_minfit.o \ eis_ortbak.o eis_orthes.o eis_ortran.o eis_pythag.o eis_qzhes.o \ eis_qzit.o eis_qzval.o eis_qzvec.o eis_ratqr.o eis_rebak.o \ eis_rebakb.o eis_reduc.o eis_reduc2.o eis_rg.o eis_rgg.o \ eis_rs.o eis_rsb.o eis_rsg.o eis_rsgab.o eis_rsgba.o \ eis_rsm.o eis_rsp.o eis_rst.o eis_rt.o eis_svd_slow.o eis_svd.o \ eis_tinvit.o eis_tql1.o eis_tql2.o eis_tqlrat.o eis_trbak1.o \ eis_trbak3.o eis_tred1.o eis_tred2.o eis_tred3.o \ eis_tridib.o eis_tsturm.oNETCDF_OBJS = netcdf_attr.o netcdf_dim.o netcdf_error.o netcdf_libvers.o \ netcdf_nc.o netcdf_ncio.o netcdf_ncx.o netcdf_putget.o \ netcdf_string.o netcdf_v1hpg.o netcdf_v2i.o netcdf_var.o \ thd_mincread.oSUMA_OBJS = suma_afni_surface.o suma_datasets.o suma_algorithms.oMISC_OBJS = afni_suma.o vol2surf.o nifti1_io.o znzlib.o list_struct.o \ nifti_statlib.o nifticdf.o r_new_resam_dset.o r_idisp.o \ r_misc.o matrix.o gifti_choice.o misc_math.olibmri.a:$(NIML_OBJS) $(MRI_OBJS) $(THD_OBJS) \ $(EDT_OBJS) $(CS_OBJS) $(EIS_OBJS) $(NETCDF_OBJS) \ $(SUMA_OBJS) $(MISC_OBJS) niml.h mrilib.h 3ddata.h $(SOMEAFOBJS) $(RM) $@ $(AR) q libmri.a $(MRI_OBJS) $(THD_OBJS) $(EDT_OBJS) \ $(NIML_OBJS) $(CS_OBJS) $(EIS_OBJS) $(NETCDF_OBJS) \ $(SUMA_OBJS) $(MISC_OBJS) $(SOMEAFOBJS) $(RANLIB) libmri.alibmrix.so:$(IMOBJS) imseq.h display.h xim.h bbox.h xutil.h $(RM) $@ $(CC) -shared -fPIC -o libmrix.so $(IMOBJS)### Dependencies for abovethd_compress.o:thd_compress.hmcw_glob.o:mcw_glob.hthd_iochan.o:thd_iochan.hmcw_malloc.o:mcw_malloc.hafni_environ.o:afni_environ.hvol2surf.o:vol2surf.h#################################################################### shared objects (go into the shared_lib directory)# same as .a, but build as a shared objectlibmri.so:$(NIML_OBJS) $(MRI_OBJS) $(THD_OBJS) \ $(EDT_OBJS) $(CS_OBJS) $(EIS_OBJS) $(NETCDF_OBJS) \ $(SUMA_OBJS) $(MISC_OBJS) $(SOMEAFOBJS) niml.h mrilib.h 3ddata.h \ shared_netcdf_attr $(RM) $@ $(CC) -shared -fPIC -o libmri.so $(MRI_OBJS) $(THD_OBJS) $(EDT_OBJS) \ $(NIML_OBJS) $(CS_OBJS) $(EIS_OBJS) $(NETCDF_OBJS) \ $(SUMA_OBJS) $(MISC_OBJS) $(SOMEAFOBJS) $(RM) netcdf_attr.o# remake netcdf objects with PICshared_netcdf_attr: $(RM) netcdf_attr.o $(MAKE) netcdf_attr.o CCMIN="${CCMIN} -fPIC"# same as .a, but build as a shared objectlibmrix.a:$(IMOBJS) imseq.h display.h xim.h bbox.h xutil.h $(RM) libmrix.a $(AR) q libmrix.a $(IMOBJS) $(RANLIB) libmrix.ashared_objs: $(INSTALLDIR) libmri.so libmrix.so $(MV) libmri.so libmrix.so $(INSTALLDIR)#################################################################### Plugin stuff.SUFFIXES:.$(PLUGIN_SUFFIX)SO = $(PLUGIN_SUFFIX)plugins:plug_clust.$(SO) plug_copy.$(SO) plug_rename.$(SO) \ plug_tag.$(SO) plug_power.$(SO) plug_stats.$(SO) \ plug_lsqfit.$(SO) plug_imreg.$(SO) plug_edit.$(SO) \ plug_nlfit.$(SO) plug_realtime.$(SO) plug_3ddot.$(SO) \ plug_coorder.$(SO) plug_compress.$(SO) plug_volreg.$(SO) \ plug_drawdset.$(SO) plug_maskave.$(SO) plug_deconvolve.$(SO) \ plug_render.$(SO) plug_notes.$(SO) plug_histog.$(SO) \ plug_scatplot.$(SO) plug_nudge.$(SO) plug_wavelets.$(SO) \ plug_second_dataset.$(SO) plug_betafit.$(SO) \ plug_zeropad.$(SO) plug_nth_dataset.$(SO) \ plug_roiplot.$(SO) plug_ttget.$(SO) plug_L1fit.$(SO) \ plug_3ddup.$(SO) plug_histog_multi.$(SO) \ plug_afnihistory.$(SO) \ models contrib_pluginsmodels: model_constant.$(SO) model_linear.$(SO) model_quadratic.$(SO) \ model_null.$(SO) model_diffusion.$(SO) model_beta.$(SO) \ model_sinewave_ap.$(SO) model_sinewave_apf.$(SO) \ model_squarewave_ap.$(SO) model_squarewave_apf.$(SO) \ model_trnglwave_ap.$(SO) model_trnglwave_apf.$(SO) \ model_exp.$(SO) model_diffexp.$(SO) model_gammavar.$(SO) \ model_convgamma.$(SO) model_convgamma2a.$(SO) \ model_michaelis_menton.$(SO) model_linplusort.$(SO) \ model_zero.$(SO) model_demri_3.$(SO) model_expr2.$(SO) \ model_conv_diffgamma.$(SO) model_expMEMRI.$(SO) \ model_expMEMRI3.$(SO)# Contributed plugins go last, since they might not compile wellcontrib_plugins: ziad_plugins birn_plugins kummer_plugins laconte_plugins \ rickr_plugins tross_plugins belmonte_plugins fredtam_plugins \ davidshin_pluginsziad_plugins: plug_3Ddump_V2.$(SO) plug_4Ddump.$(SO) \ plug_delay_V2.$(SO) plug_extract.$(SO)fredtam_plugins: plug_retroicor.$(SO)davidshin_plugins: plug_aslA3D3.$(SO)birn_plugins: plug_stavg.$(SO)kummer_plugins: plug_reorder.$(SO)rickr_plugins: plug_roiedit.$(SO) plug_hemisub.$(SO) \ plug_maskcalc.$(SO) plug_maxima.$(SO) \ plug_crender.$(SO) plug_vol2surf.$(SO)tross_plugins: plug_fourier.$(SO)belmonte_plugins: plug_threshold.$(SO) plug_permtest.$(SO)laconte_plugins: plug_3dsvm.$(SO)install_plugins: $(INSTALLDIR) $(MV) *.$(PLUGIN_SUFFIX) $(INSTALLDIR) mkdir -p $(INSTALLDIR)/funstuff $(CP) faces/face_*.jpg faces/splash_*.jpg poems/poem_*.txt $(INSTALLDIR)/funstuff echo Plugins put in directory $(INSTALLDIR): echo Do not forget to setenv AFNI_PLUGINPATH appropriately.c.$(SO):afni_plugin.h afni.h 3ddata.h $(RM) $@ $(PLUGIN_CC) -c $*.c $(INFLAGS) $(LD) $(PLUGIN_LFLAGS) -o $*.$(SO) $*.oplug_realtime.$(SO):plug_realtime.c $(RM) $@ $(PLUGIN_CC) -c plug_realtime.c $(INFLAGS) $(LD) $(PLUGIN_LFLAGS) -o plug_realtime.$(SO) plug_realtime.oplug_drealtime.$(SO):plug_realtime.c $(RM) $@ $(PLUGIN_CCD) -c plug_realtime.c $(INFLAGS) $(LD) $(PLUGIN_LFLAGS) -o plug_drealtime.$(SO) plug_realtime.oplug_crender.$(SO):plug_crender.c $(RM) $@ $(PLUGIN_CC) -c plug_crender.c $(INFLAGS) $(LD) $(PLUGIN_LFLAGS) -o plug_crender.$(SO) plug_crender.o -L.plug_maxima.$(SO):plug_maxima.c maxima.o $(RM) $@ $(PLUGIN_CC) -c plug_maxima.c $(INFLAGS) $(LD) $(PLUGIN_LFLAGS) -o plug_maxima.$(SO) plug_maxima.o maxima.o -L.### From Fred Tamplug_retroicor.$(SO):plug_retroicor.c retroicor.o $(RM) $@ $(PLUGIN_CC) -c plug_retroicor.c $(INFLAGS) $(LD) $(PLUGIN_LFLAGS) -o plug_retroicor.$(SO) plug_retroicor.o \ retroicor.o# nuke any existing renderer pluginplug_render.$(SO):plug_null.o $(LD) $(PLUGIN_LFLAGS) -o plug_render.$(SO) plug_null.o### From Stephen LaConteplug_3dsvm.$(SO): ( cd svm; \ $(RM) ../$@ ; \ $(PLUGIN_CC) -c plug_3dsvm.c 3dsvm_common.c svm_common.c \ svm_learn.c svm_hideo.c $(ISFLAGS) -I.. ; \ $(LD) $(PLUGIN_LFLAGS) -o plug_3dsvm.$(SO) \ plug_3dsvm.o 3dsvm_common.o svm_common.o svm_learn.o \ svm_hideo.o -L. -L.. ; \ $(MV) plug_3dsvm.so ../. ; \ cd .. ; )# Stuff for plugins on CYGWIN:# Each plugin must be listed here and have 2 corresponding lines in fixed_plugins.h## plug_nlfit.fixed and plug_wavelets.fixed have been removed due to difficultiesPLUGIN_FIXED = plug_clust.fixed plug_copy.fixed plug_rename.fixed \ plug_tag.fixed plug_power.fixed plug_stats.fixed \ plug_lsqfit.fixed plug_imreg.fixed plug_edit.fixed \ plug_realtime.fixed plug_3ddot.fixed \ plug_coorder.fixed plug_compress.fixed plug_volreg.fixed \ plug_drawdset.fixed plug_maskave.fixed plug_deconvolve.fixed \ plug_render.fixed plug_notes.fixed plug_histog.fixed \ plug_scatplot.fixed plug_nudge.fixed \ plug_zeropad.fixed plug_3Ddump_V2.fixed \ plug_4Ddump.fixed plug_delay_V2.fixed plug_extract.fixed \ plug_betafit.fixed plug_roiplot.fixed \ plug_second_dataset.fixed \ plug_stavg.fixed plug_reorder.fixed \ plug_roiedit.fixed plug_hemisub.fixed plug_maskcalc.fixed \ plug_fourier.fixed plug_threshold.fixed \ plug_permtest.fixedplugin_fixed:$(PLUGIN_FIXED).SUFFIXES:.fixed.c.fixed:afni_plugin.h afni.h 3ddata.h $(RM) $@ $(PLUGIN_CC) -c $*.c $(INFLAGS) -DPLUGIN_init=PLUGIN_init_$* $(MV) $*.o $*.fixed# Miscellaneous stuff (plugouts)plugout_tt:plugout_tt.o $(RM) $@ $(CC) -o plugout_tt plugout_tt.o $(LFLAGS) $(LLIBS)plugout_ijk:plugout_ijk.o $(RM) $@ $(CC) -o plugout_ijk plugout_ijk.o $(LFLAGS) $(LLIBS)plugout_tta:plugout_tta.o $(RM) $@ $(CC) -o plugout_tta plugout_tta.o $(LFLAGS) $(LLIBS)plugout_surf:plugout_surf.o $(RM) $@ $(CC) -o plugout_surf plugout_surf.o $(LFLAGS) -lcurses $(LLIBS)plugout_drive:plugout_drive.o $(RM) $@ $(CC) -o plugout_drive plugout_drive.o $(LFLAGS) $(LLIBS)plugout_graph:plugout_graph.o $(RM) $@ $(CC) -o plugout_graph plugout_graph.o $(LFLAGS) $(LLIBS)####################################################################### Stuff that was originally in Fortranf2c: ( cd f2cdir ; \ $(MAKE) f2c clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' 'CCMIN=$(CCMIN)' \ 'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \ $(MV) f2c .. ; )libf2c.a: ( cd f2cdir ; \ $(MAKE) libf2c.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \ 'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \ $(MV) libf2c.a .. ; )f2c.h: $(CP) f2cdir/f2c.h ./f2c.tgz: $(TAR) cf - ./f2cdir | $(GZIP) -9v > f2c.tgz######## dlcompatlibdl.a:dlcompat/dlfcn.h dlcompat/dlopen.c ( cd dlcompat ; \ $(MAKE) libdl.a ; \ $(CP) libdl.a dlfcn.h .. ; \ cd .. ; \ $(RANLIB) libdl.a ; )######## plotting librarylibcoxplot.a:coxplot.h ( cd coxplot ; \ $(MAKE) libcoxplot.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \ 'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \ $(MV) libcoxplot.a .. ; )coxplot.h:coxplot/coxplot.h $(CP) coxplot/coxplot.h ./coxplot.tgz: $(TAR) cf - ./coxplot | $(GZIP) -9v > coxplot.tgz######## rickr objects3dresample.o: rickr/3dresample.c $(RM) $@ $(CC) -c rickr/3dresample.c $(INFLAGS)r_new_resam_dset.o: rickr/r_new_resam_dset.c rickr/r_new_resam_dset.h $(RM) $@ $(CC) -c rickr/r_new_resam_dset.c $(INFLAGS)r_idisp.o: rickr/r_idisp.c rickr/r_idisp.h $(RM) $@ $(CC) -c rickr/r_idisp.c $(INFLAGS)r_misc.o: rickr/r_misc.c rickr/r_misc.h $(RM) $@ $(CC) -c rickr/r_misc.c $(INFLAGS)######## rickr programs3dmaxima: 3dmaxima.o maxima.o libmri.a $(RM) $@ $(CC) -o 3dmaxima 3dmaxima.o maxima.o $(LFLAGS) $(LLIBS)3dresample: 3dresample.o libmri.a $(RM) $@ $(CC) -o 3dresample 3dresample.o $(LFLAGS) $(LLIBS)file_tool: ge4_header.o ( cd rickr ; \ $(MAKE) file_tool 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)' \ 'LFLAGS=$(LFLAGS)' 'LLIBS=$(LLIBS)' ; \ $(MV) file_tool .. ; )Dimon: rickr/Dimon.c rickr/Imon.h rickr/realtime.c rickr/realtime.h ( cd rickr ; \ $(MAKE) Dimon 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)' \ 'LFLAGS=$(LFLAGS)' 'EXTRA_LIBS_2=$(EXTRA_LIBS_2)' \ 'LGIFTI=$(LGIFTI)' ; \ $(MV) Dimon .. ; )Imon: rickr/Imon.c rickr/Imon.h rickr/realtime.c rickr/realtime.h thd_iochan.o ( cd rickr ; \ $(MAKE) Imon 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)' \ 'LFLAGS=$(LFLAGS)' 'EXTRA_LIBS_2=$(EXTRA_LIBS_2)' ; \ $(MV) Imon .. ; )serial_helper: rickr/serial_helper.c ( cd rickr ; \ $(MAKE) serial_helper 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)' \ 'LFLAGS=$(LFLAGS)' 'EXTRA_LIBS_2=$(EXTRA_LIBS_2)' ; \ $(MV) serial_helper .. ; )serial_writer: rickr/serial_writer.c $(RM) $@ $(CCMIN) -o serial_writer rickr/serial_writer.cgtest: ( cd gifti ; \ $(MAKE) gtest 'RM=$(RM)' 'CC=$(CC)' 'IFLAGS=$(ISFLAGS)' \ 'LFLAGS=$(LFLAGS)' ; \ $(MV) gtest .. ; )3dmatmult: 3dmatmult.o libmri.a $(RM) $@ $(CC) -o 3dmatmult 3dmatmult.o $(LFLAGS) $(LLIBS)3dmask_tool: 3dmask_tool.o libmri.a $(RM) $@ $(CC) -o 3dmask_tool 3dmask_tool.o $(LFLAGS) $(LLIBS)column_cat: rickr/column_cat.c $(RM) $@ $(CC) -o column_cat rickr/column_cat.c######## rendering librarylibvolpack.a: ( cd volpack ; \ $(MAKE) libvolpack.a clean 'RM=$(RM)' 'CC=$(CCVOL)' 'AR=$(AR)' \ 'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \ $(MV) libvolpack.a .. ; )volpack.h: $(CP) volpack/volpack.h ./volpack.tgz: $(TAR) cf - ./volpack | $(GZIP) -9v > volpack.tgz######## for Larry Frankqhull: ( cd qhulldir ; \ $(MAKE) qhull rbox qdelaunay clean \ 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \ $(MV) qhull rbox qdelaunay .. ; )# CYGWIN: we "mv" the result, so must name it correctly as qhull.exeqhull.exe: ( cd qhulldir ; \ $(MAKE) qhull clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \ $(MV) qhull.exe .. ; )######## 3DEdge library files - make them and move them up herelib3DEdge.a: ( cd 3DEdge/src ; $(MAKE) clean lib3DEdge.a 'RM=$(RM)' 'AR=$(AR)' 'RANLIB=$(RANLIB)' 'CC=$(CCFAST)' 'IFLAGS=$(ISFLAGS)' 'LFLAGS=$(LFLAGS)' ; $(MV) *.a ../.. ; )######## Eispack and CDF library files - make them and move them up hereeis_bakvec.o: ( cd eispack/ ; $(MAKE) all 'CC=$(CCFAST)' 'CCSVD=$(CCSVD)' ; $(MV) *.o .. ; )######## Ditto for NIML objects$(NIML_OBJS):niml.h ( cd niml/ ; $(MAKE) all 'CC=$(CC)' ; $(MV) *.o .. ; )niml.h:niml/niml.h $(CP) niml/niml.h .######## netcdf library files - make them and move them up herenetcdf_attr.o: ( cd netcdf-3.5.0/src ; \ FC="" ; export FC ; F90="" ; export F90 ; \ CXX="" ; export CXX ; CC="${CCMIN}";export CC; \ $(RM) config.cache config.log config.status ; \ chmod ugo+x ./configure ; \ ./configure ; $(MAKE) libsrc/all ; \ $(CP) libsrc/netcdf.h ../.. ; \ $(MV) libsrc/attr.o ../../netcdf_attr.o ; \ $(MV) libsrc/dim.o ../../netcdf_dim.o ; \ $(MV) libsrc/error.o ../../netcdf_error.o ; \ $(MV) libsrc/libvers.o ../../netcdf_libvers.o ; \ $(MV) libsrc/nc.o ../../netcdf_nc.o ; \ $(MV) libsrc/ncio.o ../../netcdf_ncio.o ; \ $(MV) libsrc/ncx.o ../../netcdf_ncx.o ; \ $(MV) libsrc/putget.o ../../netcdf_putget.o ; \ $(MV) libsrc/string.o ../../netcdf_string.o ; \ $(MV) libsrc/v1hpg.o ../../netcdf_v1hpg.o ; \ $(MV) libsrc/v2i.o ../../netcdf_v2i.o ; \ $(MV) libsrc/var.o ../../netcdf_var.o ; \ $(RM) config.cache config.log config.status ; \ $(MAKE) clean ; )######## 27 Jul 2001 - for fungifsicle: ( cd gifsicledir ; \ $(MAKE) gifsicle clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' ; \ $(MV) gifsicle .. ; )######## 02 Aug 2001 - for funmpeg_encode: ( cd mpeg_encodedir ; \ $(MAKE) mpeg_encode clean 'RM=$(RM)' 'CC=$(CC)' 'LFLAGS=$(LFLAGS)' 'LLIBS=$(LLIBS)' ; \ $(MV) mpeg_encode .. ; )######## 03 Dec 2003 - for even more funmpegtoppm: ( cd mpegtoppm_dir ; chmod ugo+x ./configure ; \ ./configure --disable-sdl --disable-mlib --without-x --disable-dependency-tracking --disable-accel-detect ; \ $(MAKE) ; mv doc/sample2 ../mpegtoppm ; $(MAKE) clean ; )######## 11 Sep 2002 - for fundjpeg:cjpeglibjpeg.a:cjpegcjpeg: ( cd jpeg-6b ; $(RM) Makefile jconfig.h ; \ chmod ugo+x ./configure ; ./configure 'CC=$(CCMIN)' ; \ $(MAKE) ; $(MV) cjpeg djpeg libjpeg.a .. ; \ $(MAKE) clean ; $(RM) Makefile )libXmHTML.a: ( cd XmHTML ; make lib 'CC=$(CC)' 'II=$(IFLAGS)' ; \ $(MV) lib/libXmHTML.a .. ; make clean )thd_xwebber.o:thd_xwebber.c $(CC) -c thd_xwebber.c -I./XmHTML/include $(INFLAGS)######## FFTW - not usedlibfftw.a: ( cd fftw ; \ $(MAKE) libfftw.a clean 'RM=$(RM)' 'CC=$(CCFAST)' 'AR=$(AR)' \ 'RANLIB=$(RANLIB)' 'LDFLAGS=$(LDFLAGS)' 'IFLAGS=$(ISFLAGS)' ; \ $(MV) libfftw.a .. ; )fftw.h: $(CP) fftw/fftw.h ./fftw_setup:fftw_setup.o $(CC) -o fftw_setup fftw_setup.o $(LFLAGS) -lfftw $(LLIBS)######## CLAMS - not usedlibclam.a: ( cd clamdir ; \ $(MAKE) libclam.a clean 'RM=$(RM)' 'CC=$(CC)' 'AR=$(AR)' \ 'RANLIB=$(RANLIB)' 'IFLAGS=-I..' ; \ $(MV) libclam.a .. ; )libclam.h: $(CP) clamdir/libclam.h ./clamsrc.tgz: $(TAR) cf - ./clamsrc | $(GZIP) -9v > clamsrc.tgzclamdir.tgz: $(TAR) cf - ./clamdir | $(GZIP) -9v > clamdir.tgz######### The following line only needs to be used if parser.f## is edited, since AFNI ships with parser.c already made.parser.c: $(F2C) parser.f## expression parsing and evaluation functionsparser.o:parser.c f2c.h libf2c.a $(CCFAST) -c parser.c $(INFLAGS)## programs that user parser.c functionsccalc:parser.o parser_int.o ccalc.o $(RM) $@ $(CC) -o ccalc ccalc.o parser.o parser_int.o $(LFLAGS) $(LLIBS)1deval:parser.o parser_int.o 1deval.o $(RM) $@ $(CC) -o 1deval 1deval.o parser.o parser_int.o $(LFLAGS) $(LLIBS)1dmatcalc:parser.o parser_int.o 1dmatcalc.o mri_matrix.o $(RM) $@ $(CC) -o 1dmatcalc 1dmatcalc.o parser.o parser_int.o $(LFLAGS) $(LLIBS)3dmatcalc:parser.o parser_int.o 3dmatcalc.o $(RM) $@ $(CC) -o 3dmatcalc 3dmatcalc.o parser.o parser_int.o $(LFLAGS) $(LLIBS)colfit.c: $(F2C) colfit.fcolcalc.c: $(F2C) colcalc.fcolfit:parser.o colfit.o $(CC) -o colfit colfit.o parser.o $(LFLAGS) -lclam $(LLIBS)colcalc:parser.o colcalc.o $(CC) -o colcalc colcalc.o parser.o $(LFLAGS) -lclam $(LLIBS)imcalc:imcalc.o parser.o parser_int.o $(CC) -o imcalc imcalc.o parser.o parser_int.o $(LFLAGS) $(LLIBS)AFNI_HIST_FILES = afni_history.c \ afni_history_bpittman.c afni_history_christip.c afni_history_dglen.c \ afni_history_gangc.c afni_history_rickr.c afni_history_rwcox.c \ afni_history_ziad.cafni_history: $(AFNI_HIST_FILES) $(RM) $@ $(CCMIN) -o afni_history $(AFNI_HIST_FILES)############################################################################ Miscellaneous programs, mostly for testing purposesfftest:fftest.o $(CC) -o fftest fftest.o $(LFLAGS) $(LLIBS)fftwest:fftest.c $(CC) -o fftwest fftest.c -DUSE_FFTW $(LFLAGS) -lfftw $(LLIBS)fftnext:fftnext.o $(CC) -o fftnext fftnext.o $(LFLAGS) $(LLIBS)fftcheck:fftcheck.o $(CC) -o fftcheck fftcheck.o $(LFLAGS) $(LLIBS)fftest_dj:fftest_dj.o csfft_dj.o fft_dj.o $(CC) -o fftest_dj fftest_dj.o csfft_dj.o fft_dj.o $(LFLAGS) $(LLIBS)fftprint:fftprint.o $(CC) -o fftprint fftprint.o $(LFLAGS) $(LLIBS)## get a Web page using the command linemyget:myget.o $(CC) -o myget myget.o $(LFLAGS) $(LLIBS)## zero out before removingrmz:rmz.o $(CC) -o rmz rmz.o $(LFLAGS) $(LLIBS)uncomment:uncomment.o $(CC) -o uncomment uncomment.o $(LFLAGS) $(LLIBS)help_format:help_format.o $(CC) -o help_format help_format.oibinom:ibinom.o $(CC) -o ibinom ibinom.o $(LFLAGS) $(LLIBS)## GIF animationwhirlgif:whirlgif.h whirlgif.c $(CC) -o whirlgif whirlgif.c $(INFLAGS) $(LFLAGS) $(LLIBS)extor.o:extor.c $(CCFAST) -c extor.c $(INFLAGS)ktaub.o:ktaub.c $(CCFAST) -c ktaub.c $(INFLAGS)bilinear_warp3D.o:bilinear_warp3D.c $(CCFAST) -c bilinear_warp3D.c $(INFLAGS)thd_detrend.o:thd_detrend.c $(CCFAST) -c thd_detrend.c $(INFLAGS)thd_bandpass.o:thd_bandpass.c $(CCFAST) -c thd_bandpass.c $(INFLAGS)thd_dset_to_vectim.o:thd_dset_to_vectim.c $(CCFAST) -c thd_dset_to_vectim.c $(INFLAGS)thd_ttest.o:thd_ttest.c $(CCFAST) -c thd_ttest.c $(INFLAGS)extor:extor.o $(CC) -o extor extor.o $(INFLAGS) $(LFLAGS) $(LLIBS)exx.o:exx.c $(CCFAST) -c exx.c $(INFLAGS)exx:exx.o $(CC) -o exx exx.o $(INFLAGS) $(LFLAGS) $(LLIBS)mycat:mycat.o $(CC) -o mycat mycat.o $(LFLAGS)qqq.o:qqq.c $(CCFAST) -c qqq.c $(INFLAGS)qqq:qqq.o $(CC) -o qqq qqq.o $(INFLAGS) $(LFLAGS) -lmrix -lcoxplot $(LLIBS)warping.o:warping.c $(CCFAST) -c warping.c $(INFLAGS)warping:warping.o $(CC) -o warping warping.o $(INFLAGS) $(LFLAGS) $(LLIBS)mri_gwarp.o:mri_gwarp.c $(CCFAST) -c mri_gwarp.c $(INFLAGS)gwarp:mri_gwarp.o $(CC) -o gwarp mri_gwarp.o $(INFLAGS) $(LFLAGS) $(LLIBS)3dMaskToASCII.o:3dMaskToASCII.c $(CC) -c 3dMaskToASCII.c $(INFLAGS)3dMaskToASCII:3dMaskToASCII.o $(CC) -o 3dMaskToASCII 3dMaskToASCII.o $(INFLAGS) $(LFLAGS) $(LLIBS)bitvec.o:bitvec.c $(CCFAST) -c bitvec.c $(INFLAGS)bitvec:bitvec.o $(CC) -o bitvec bitvec.o $(INFLAGS) $(LFLAGS) $(LLIBS)unu.o:unu.c $(CCFAST) -c unu.c $(INFLAGS)unu:unu.o $(CC) -o unu unu.o $(INFLAGS) $(LFLAGS) $(LLIBS)Xphace:Xphace.o $(CC) -o Xphace Xphace.o $(INFLAGS) $(LFLAGS) -lmrix -lcoxplot $(LLIBS)3dbetafit:3dbetafit.o betafit.c $(CC) -o 3dbetafit 3dbetafit.o $(INFLAGS) $(LFLAGS) $(LLIBS)3dbetafit2.o:3dbetafit2.c $(CCFAST) -c 3dbetafit2.c $(INFLAGS)pv.o:pv.c $(CCFAST) -c pv.c $(INFLAGS)3dbetafit2:3dbetafit2.o betafit.c $(CC) -o 3dbetafit2 3dbetafit2.o $(INFLAGS) $(LFLAGS) $(LLIBS)3dbetafit3:3dbetafit3.o betafit.c $(CC) -o 3dbetafit3 3dbetafit3.o $(INFLAGS) $(LFLAGS) $(LLIBS)testcox:testcox.o $(CC) -o testcox testcox.o $(INFLAGS) $(LFLAGS) $(LLIBS)agni_to_afni:agni_to_afni.o agni.o $(CC) -o agni_to_afni agni_to_afni.o $(INFLAGS) $(LFLAGS) $(LLIBS)epsim:epsim.o $(RM) $@ $(CC) -o epsim epsim.o $(LFLAGS) $(LLIBS)nimltest:nimltest.o niml.h $(RM) $@ $(CC) -o nimltest nimltest.o $(LFLAGS) $(LLIBS)nimel:nimel.o niml.h $(RM) $@ $(CC) -o nimel nimel.o $(LFLAGS) $(LLIBS)nidset:nidset.o niml.h $(RM) $@ $(CC) -o nidset nidset.o $(LFLAGS) $(LLIBS)nicat:nicat.o $(RM) $@ $(CC) -o nicat nicat.o $(LFLAGS) $(LLIBS)malp:mri_alphasim.o $(RM) $@ $(CC) -o malp mri_alphasim.o $(LFLAGS) $(LLIBS)test_rowtype:test_rowtype.o $(RM) $@ $(CC) -o test_rowtype test_rowtype.o $(LFLAGS) $(LLIBS)niccc:niccc.o $(RM) $@ $(CC) -o niccc niccc.o $(LFLAGS) $(LLIBS)aiv:aiv.o $(RM) $@ $(CC) -o aiv aiv.o $(LFLAGS) -lmrix -lcoxplot $(LLIBS)test_powell:test_powell.o $(RM) $@ $(CC) -o test_powell test_powell.o $(LFLAGS) $(LLIBS)asnap:asnap.o $(RM) $@ $(CC) -o asnap asnap.o $(LFLAGS) -lmrix -lcoxplot $(LLIBS)galler:galler.o $(RM) $@ $(CC) -o galler galler.o $(LFLAGS) $(LLIBS)# specifics for the nifti library files3dAFNItoNIFTI.o:3dAFNItoNIFTI.c $(RM) $@ $(CC) -c 3dAFNItoNIFTI.c $(INFLAGS)3dAFNItoNIFTI:3dAFNItoNIFTI.o nifti1_io.o znzlib.o $(RM) $@ $(CC) -o 3dAFNItoNIFTI 3dAFNItoNIFTI.o nifti1_io.o znzlib.o $(LFLAGS) $(LLIBS)nifti1_io.o:nifti/niftilib/nifti1_io.c nifti/niftilib/nifti1_io.h $(RM) $@ $(CC) -c nifti/niftilib/nifti1_io.c $(INFLAGS)znzlib.o:nifti/znzlib/znzlib.c nifti/znzlib/znzlib.h $(RM) $@ $(CC) -c nifti/znzlib/znzlib.c $(INFLAGS)nifti_stats.o:nifti/utils/nifti_stats.c $(RM) $@ $(CC) -c nifti/utils/nifti_stats.c $(INFLAGS)# 64-bit gcc 4.0+ has optimization problem with this file# -> use 3.4 if necessary 19 May 2010 [rickr]nifticdf.o:nifti/nifticdf/nifticdf.c $(RM) $@ $(CCOLD) -D__COMPILE_UNUSED_FUNCTIONS__ -c nifti/nifticdf/nifticdf.c $(INFLAGS)nifti_statlib.o:nifti/utils/nifti_stats.c nifti_statlib.c $(RM) $@ $(CC) -c nifti_statlib.c -Inifti/utils $(INFLAGS)nifti_stats:nifti_stats.o nifticdf.o $(RM) $@ $(CC) -o nifti_stats nifti_stats.o nifticdf.o -lmnifti1_test.o:nifti/utils/nifti1_test.c $(RM) $@ $(CC) -c nifti/utils/nifti1_test.c $(INFLAGS)nifti1_test:nifti1_test.o nifti1_io.o znzlib.o $(RM) $@ $(CC) -o nifti1_test nifti1_test.o nifti1_io.o znzlib.o $(LZLIB) -lmnifti_tool.o:nifti/utils/nifti_tool.c $(RM) $@ $(CC) -c nifti/utils/nifti_tool.c $(INFLAGS)nifti_tool:nifti_tool.o nifti1_io.o znzlib.o $(RM) $@ $(CC) -o nifti_tool nifti_tool.o nifti1_io.o znzlib.o $(LZLIB) -lmnifti_tool.exe:nifti_tool.o nifti1_io.o znzlib.o $(RM) $@ $(CC) -o nifti_tool.exe nifti_tool.o nifti1_io.o znzlib.o $(LZLIB) -lm# just compile completely, removing issue of librariesgifti_tool:nifti1_io.o znzlib.o $(RM) $@ $(CC) -o gifti_tool $(INFLAGS) $(LFLAGS) \ gifti/gifti_tool.c gifti/gifti_io.c gifti/gifti_xml.c \ nifti1_io.o znzlib.o $(LGIFTI) $(LZLIB) -lmgifti_choice.o:gifti_choice.c thd_gifti.c suma_gifti.c $(RM) $@ $(CC) -c gifti_choice.c -Igifti $(INFLAGS)tsdsim:tsdsim.o $(RM) $@ $(CC) -o tsdsim tsdsim.o $(LFLAGS) $(LLIBS) -lmxtsdsolve:tsdsolve.c $(CC) -c tsdsolve.c -I. $(CC) -o tsdsolve tsdsolve.o $(LFLAGS) \ -llapack_panther -lblas_panther -lF77 -lI77 \ $(LLIBS)#-------------------------------------------------------------------------------##############AVOVK directory3dkmeans: avovk/3dkmeans.c avovk/cluster_floatNOMASK.c avovk/thd_segtools_fNM.c ( cd avovk ; \ ./@MakeLocalMake ;\ $(MAKE) afni_all ; \ cd ../ ; )libsegtools.a: avovk/cluster_floatNOMASK.c avovk/thd_segtools_fNM.c ( cd avovk ; \ ./@MakeLocalMake ;\ $(MAKE) libsegtools.a ; \ $(CP) libsegtools.a ../; \ cd ../ ; )##############PTAYLOR directoryptaylor_all: ( cd ptaylor ; \ ./@MakeLocalMake ;\ $(MAKE) afni_all ; \ cd ../ ; )ptaylor_install: ( cd ptaylor ; \ ./@MakeLocalMake ;\ $(MAKE) afni_install ; \ cd ../ ; )libtracktools.a: ( cd ptaylor ; \ ./@MakeLocalMake ;\ $(MAKE) clean libtracktools.a ; \ $(CP) libtracktools.a ../; \ cd ../ ; )##############PKUNDU directorypkundu_install: ( cd pkundu ; \ ./@install_pkundu $(INSTALLDIR) ;\ cd ../ ; )##############SUMAlibSUMA.a: libmri.a libmrix.a libcoxplot.a libf2c.a libtracktools.a ( cd SUMA ; \ rm -f libSUMA.a ;\ $(MAKE) -f $(SUMA_MAKEFILE_NAME) clean MarchingCubes.o libSUMA.a 'INSTALLDIR=$(INSTALLDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'RANLIB=$(RANLIB)' \ 'MAKE=$(MAKE)' \ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ; \ if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi ;\ $(CP) SUMA/libSUMA.a ${INSTALLDIR}; \ $(CP) SUMA/libSUMA.a ./; )libgts.a: ( cd SUMA ; \ rm -f libgts.a ;\ $(MAKE) -f $(SUMA_MAKEFILE_NAME) libgts.a ; \ cd ../ ; \ if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi ;\ $(CP) SUMA/libgts.a ${INSTALLDIR}; \ $(CP) SUMA/libgts.a ./; )libSUMAseg.a: ( cd SUMA ; \ rm -f libSUMAseg.a ;\ $(MAKE) -f $(SUMA_MAKEFILE_NAME) libSUMAseg.a ; \ cd ../ ; \ if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi ;\ $(CP) SUMA/libSUMAseg.a ${INSTALLDIR}; \ $(CP) SUMA/libSUMAseg.a ./; )libGLws.a: ( cd SUMA ; \ rm -f libGLws.a ;\ $(MAKE) -f $(SUMA_MAKEFILE_NAME) libGLws.a 'INSTALLDIR=$(INSTALLDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'RANLIB=$(RANLIB)' \ 'MAKE=$(MAKE)' \ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ; \ if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi ;\ $(CP) SUMA/libGLws.a ${INSTALLDIR}; \ $(CP) SUMA/libGLws.a ./; )####link executables but check for libraries first and create them if needed suma_exec:libGLws.a libSUMA.a libtracktools.a libmri.a xutil.o LiteClue.o parser.o parser_int.o libmrix.a libcoxplot.a libf2c.a ( cd SUMA ; \ $(MAKE) -f $(SUMA_MAKEFILE_NAME) testGL suma ScaleToMap CompareSurfaces \ MakeColorMap ROI2dataset 3dVol2Surf \ 3dSurf2Vol SurfMeasures SurfFWHM \ ConvertSurface ConvertDset SurfClust IsoSurface \ ConvexHull MapIcosahedron CreateIcosahedron SurfaceMetrics \ SurfSmooth inspec quickspec FSread_annot SurfPatch SurfQual SampBias \ 3dSkullStrip 3dCRUISEtoAFNI 3dBRAIN_VOYAGERtoAFNI 3dSurfMask\ SurfToSurf Surf2VolCoord ROIgrow SurfDsetInfo SurfInfo AnalyzeTrace \ DriveSuma SurfDist SpharmReco SpharmDeco prompt_user SurfRetinoMap \ ParseName 3dGenPriors 3dSeg SurfExtrema 3dinfill 3dHist \ 'INSTALLDIR=$(INSTALLDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \ 'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \ 'RANLIB=$(RANLIB)' \ 'MAKE=$(MAKE)' \ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ;)####Do the GTS related stuff suma_gts_progs: libgts.a ( cd SUMA ; \ $(MAKE) -f $(SUMA_MAKEFILE_NAME) SurfMesh 'INSTALLDIR=$(INSTALLDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \ 'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \ 'RANLIB=$(RANLIB)' \ 'MAKE=$(MAKE)' \ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ;)####run make all in SUMA directory, USE FOR DEVELOPMENT ONLY suma_all:libmri.a libtracktools.a xutil.o LiteClue.o parser.o parser_int.o libmrix.a libcoxplot.a libf2c.a ( cd SUMA ; \ $(MAKE) -f $(SUMA_MAKEFILE_NAME) all 'INSTALLDIR=$(INSTALLDIR)' 'INSTALLDIR_SUMA=$(INSTALLDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \ 'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \ 'RANLIB=$(RANLIB)' \ 'MAKE=$(MAKE)' \ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ;)####run make anew in SUMA directory, USE FOR DEVELOPMENT ONLY suma_anew:libmri.a xutil.o LiteClue.o parser.o parser_int.o libmrix.a libcoxplot.a libf2c.a libtracktools.a ( cd SUMA ; \ $(MAKE) -f $(SUMA_MAKEFILE_NAME) anew 'INSTALLDIR=$(INSTALLDIR)' 'INSTALLDIR_SUMA=$(INSTALLDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \ 'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \ 'RANLIB=$(RANLIB)' \ 'MAKE=$(MAKE)' \ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)' \ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ;)suma_clean: $(RM) SUMA/libSUMA.a libSUMA.a SUMA/libGLws.a libGLws.a if [ -f SUMA/suma ]; then $(RM) SUMA/suma; fi; if [ -f suma ]; then $(RM) suma; fi; if [ -f SUMA/MakeColorMap ]; then $(RM) SUMA/MakeColorMap; fi; if [ -f MakeColorMap ]; then $(RM) MakeColorMap; fi; if [ -f SUMA/ROI2dataset ]; then $(RM) SUMA/ROI2dataset; fi; if [ -f ROI2dataset ]; then $(RM) ROI2dataset; fi; if [ -f SUMA/3dVol2Surf ]; then $(RM) SUMA/3dVol2Surf; fi; if [ -f 3dVol2Surf ]; then $(RM) 3dVol2Surf; fi; if [ -f SUMA/3dSurf2Vol ]; then $(RM) SUMA/3dSurf2Vol; fi; if [ -f 3dSurf2Vol ]; then $(RM) 3dSurf2Vol; fi; if [ -f SUMA/SurfMeasures ]; then $(RM) SUMA/SurfMeasures; fi; if [ -f SurfMeasures ]; then $(RM) SurfMeasures; fi; if [ -f SUMA/SurfFWHM ]; then $(RM) SUMA/SurfFWHM ; fi; if [ -f SurfFWHM ]; then $(RM) SurfFWHM ; fi; if [ -f ScaleToMap ]; then $(RM) ScaleToMap; fi; if [ -f SUMA/ScaleToMap ]; then $(RM) SUMA/ScaleToMap; fi; if [ -f CompareSurfaces ]; then $(RM) CompareSurfaces ; fi; if [ -f SUMA/CompareSurfaces ]; then $(RM) SUMA/CompareSurfaces ; fi; if [ -f ConvertSurface ]; then $(RM) ConvertSurface; fi; if [ -f SUMA/ConvertSurface ]; then $(RM) SUMA/ConvertSurface; fi; if [ -f ConvertDset ]; then $(RM) ConvertDset; fi; if [ -f SUMA/ConvertDset ]; then $(RM) SUMA/ConvertDset; fi; if [ -f SurfClust ]; then $(RM) SurfClust; fi; if [ -f SUMA/SurfClust ]; then $(RM) SUMA/SurfClust; fi; if [ -f IsoSurface ]; then $(RM) IsoSurface; fi; if [ -f SUMA/IsoSurface ]; then $(RM) SUMA/IsoSurface; fi; if [ -f ConvexHull ]; then $(RM) ConvexHull; fi; if [ -f SUMA/ConvexHull ]; then $(RM) SUMA/ConvexHull; fi; if [ -f SUMA_glxdino ]; then $(RM) SUMA_glxdino; fi; if [ -f SUMA_paperplane ]; then $(RM) SUMA_paperplane; fi; if [ -f SUMA/SUMA_glxdino ]; then $(RM) SUMA/SUMA_glxdino; fi; if [ -f SUMA/SUMA_paperplane ]; then $(RM) SUMA/SUMA_paperplane; fi; if [ -f SUMA_pixmap2eps ]; then $(RM) SUMA_pixmap2eps; fi; if [ -f SUMA/SUMA_pixmap2eps ]; then $(RM) SUMA/SUMA_pixmap2eps; fi; if [ -f SurfaceMetrics ]; then $(RM) SurfaceMetrics; fi; if [ -f SUMA/SurfaceMetrics ]; then $(RM) SUMA/SurfaceMetrics; fi; if [ -f inspec ]; then $(RM) inspec; fi; if [ -f SUMA/inspec ]; then $(RM) SUMA/inspec; fi; if [ -f quickspec ]; then $(RM) quickspec; fi; if [ -f SUMA/quickspec ]; then $(RM) SUMA/quickspec; fi; if [ -f FSread_annot ]; then $(RM) FSread_annot; fi; if [ -f SUMA/FSread_annot ]; then $(RM) SUMA/FSread_annot; fi; if [ -f SurfPatch ]; then $(RM) SurfPatch; fi; if [ -f SUMA/SurfPatch ]; then $(RM) SUMA/SurfPatch; fi; if [ -f SurfQual ]; then $(RM) SurfQual; fi; if [ -f SUMA/SurfQual ]; then $(RM) SUMA/SurfQual; fi; if [ -f SurfSmooth ]; then $(RM) SurfSmooth; fi; if [ -f SUMA/SurfSmooth ]; then $(RM) SUMA/SurfSmooth; fi; if [ -f MapIcosahedron ]; then $(RM) MapIcosahedron; fi; if [ -f SUMA/MapIcosahedron ]; then $(RM) SUMA/MapIcosahedron; fi; if [ -f CreateIcosahedron ]; then $(RM) CreateIcosahedron; fi; if [ -f SUMA/CreateIcosahedron ]; then $(RM) SUMA/CreateIcosahedron; fi; if [ -f SurfMesh ]; then $(RM) SurfMesh; fi; if [ -f SUMA/SurfMesh ]; then $(RM) SUMA/SurfMesh; fi; if [ -f SampBias ]; then $(RM) SampBias; fi; if [ -f SUMA/SampBias ]; then $(RM) SUMA/SampBias; fi; if [ -f 3dSkullStrip ]; then $(RM) 3dSkullStrip ; fi; if [ -f SUMA/3dSkullStrip ]; then $(RM) SUMA/3dSkullStrip ; fi; if [ -f 3dCRUISEtoAFNI ]; then $(RM) 3dCRUISEtoAFNI ; fi; if [ -f SUMA/3dCRUISEtoAFNI ]; then $(RM) SUMA/3dCRUISEtoAFNI ; fi; if [ -f 3dBRAIN_VOYAGERtoAFNI ]; then $(RM) 3dBRAIN_VOYAGERtoAFNI ; fi; if [ -f SUMA/3dBRAIN_VOYAGERtoAFNI ]; then $(RM) SUMA/3dBRAIN_VOYAGERtoAFNI ; fi; if [ -f 3dSurfMask ]; then $(RM) 3dSurfMask ; fi; if [ -f SUMA/3dSurfMask ]; then $(RM) SUMA/3dSurfMask ; fi; if [ -f SurfToSurf ]; then $(RM) SurfToSurf ; fi; if [ -f SUMA/SurfToSurf ]; then $(RM) SUMA/SurfToSurf ; fi; if [ -f Surf2VolCoord ]; then $(RM) Surf2VolCoord ; fi; if [ -f SUMA/Surf2VolCoord ]; then $(RM) SUMA/Surf2VolCoord ; fi; if [ -f ROIgrow ]; then $(RM) ROIgrow ; fi; if [ -f SUMA/ROIgrow ]; then $(RM) SUMA/ROIgrow ; fi; if [ -f SurfDsetInfo ]; then $(RM) SurfDsetInfo ; fi; if [ -f SUMA/SurfDsetInfo ]; then $(RM) SUMA/SurfDsetInfo ; fi; if [ -f SurfInfo ]; then $(RM) SurfInfo ; fi; if [ -f SUMA/SurfInfo ]; then $(RM) SUMA/SurfInfo ; fi; if [ -f AnalyzeTrace ]; then $(RM) AnalyzeTrace ; fi; if [ -f SUMA/AnalyzeTrace ]; then $(RM) SUMA/AnalyzeTrace ; fi; if [ -f DriveSuma ]; then $(RM) DriveSuma ; fi; if [ -f SUMA/DriveSuma ]; then $(RM) SUMA/DriveSuma ; fi; if [ -f SurfDist ]; then $(RM) SurfDist; fi; if [ -f SUMA/SurfDist ]; then $(RM) SUMA/SurfDist; fi; if [ -f SpharmReco ]; then $(RM) SpharmReco; fi; if [ -f SUMA/SpharmReco ]; then $(RM) SUMA/SpharmReco; fi; if [ -f SpharmDeco ]; then $(RM) SpharmDeco; fi; if [ -f SUMA/SpharmDeco ]; then $(RM) SUMA/SpharmDeco; fi; if [ -f prompt_user ]; then $(RM) prompt_user; fi; if [ -f SUMA/prompt_user ]; then $(RM) SUMA/prompt_user; fi; if [ -f SurfRetinoMap ]; then $(RM) SurfRetinoMap; fi; if [ -f SUMA/SurfRetinoMap ]; then $(RM) SUMA/SurfRetinoMap; fi; if [ -f ParseName ]; then $(RM) ParseName; fi; if [ -f SUMA/ParseName ]; then $(RM) SUMA/ParseName; fi; if [ -f 3dGenPriors ]; then $(RM) 3dGenPriors; fi; if [ -f SUMA/3dGenPriors ]; then $(RM) SUMA/3dGenPriors; fi; if [ -f 3dSeg ]; then $(RM) 3dSeg; fi; if [ -f SUMA/3dSeg ]; then $(RM) SUMA/3dSeg; fi; if [ -f SurfExtrema ]; then $(RM) SurfExtrema; fi; if [ -f SUMA/SurfExtrema ]; then $(RM) SUMA/SurfExtrema; fi; if [ -f 3dinfill ]; then $(RM) 3dinfill; fi; if [ -f SUMA/3dinfill ]; then $(RM) SUMA/3dinfill; fi; if [ -f 3dHist ]; then $(RM) 3dHist; fi; if [ -f SUMA/3dHist ]; then $(RM) SUMA/3dHist; fi;####Use precompiled libraries present in SUMA/$(SUMA_BIN_ARCHIVE) and just link SUMAsuma_link: ( cd SUMA ; \ tar -xf $(SUMA_BIN_ARCHIVE) ;\ touch *.a ;\ $(CP) libmri.a libtractools.a libmrix.a libcoxplot.a libf2c.a ../ ;\ $(RM) suma MakeColorMap ROI2dataset 3dVol2Surf 3dSurf2Vol \ SurfMeasures SurfFWHM \ ScaleToMap MapIcosahedron \ CreateIcosahedron CompareSurfaces ConvertSurface ConvertDset SurfClust \ IsoSurface ConvexHull SurfaceMetrics SurfSmooth inspec \ quickspec FSread_annot SurfPatch SurfQual SampBias 3dSkullStrip \ 3dCRUISEtoAFNI 3dBRAIN_VOYAGERtoAFNI 3dSurfMask\ SurfToSurf Surf2VolCoord ROIgrow SurfDsetInfo SurfInfo AnalyzeTrace \ DriveSuma SurfDist SpharmReco SpharmDeco prompt_user SurfRetinoMap \ ParseName 3dGenPriors 3dSeg SurfExtrema 3dinfill 3dHist; \ $(MAKE) -f $(SUMA_MAKEFILE_NAME) testGL suma MakeColorMap ROI2dataset \ 3dVol2Surf 3dSurf2Vol ScaleToMap SurfMeasures SurfFWHM \ MapIcosahedron CreateIcosahedron CompareSurfaces ConvertSurface ConvertDset \ SurfClust IsoSurface ConvexHull SurfaceMetrics SurfSmooth inspec \ quickspec FSread_annot SurfPatch SurfQual SampBias 3dSkullStrip \ 3dCRUISEtoAFNI 3dBRAIN_VOYAGERtoAFNI 3dSurfMask \ SurfToSurf Surf2VolCoord ROIgrow SurfDsetInfo SurfInfo AnalyzeTrace \ DriveSuma SurfDist SpharmReco SpharmDeco prompt_user SurfRetinoMap \ ParseName 3dGenPriors 3dSeg SurfExtrema 3dinfill 3dHist \ 'INSTALLDIR=$(INSTALLDIR)' \ 'SUMA_INCLUDE_PATH=$(SUMA_INCLUDE_PATH)' \ 'SUMA_LINK_PATH=$(SUMA_LINK_PATH)' \ 'SUMA_LINK_LIB=$(SUMA_LINK_LIB)' \ 'SUMA_BIN_ARCHIVE=$(SUMA_BIN_ARCHIVE)' \ 'SUMA_GLIB_VER=$(SUMA_GLIB_VER)' \ 'RANLIB=$(RANLIB)' \ 'MAKE=$(MAKE)' \ 'CC=$(CC)' 'RM=$(RM)' 'CEXTRA=$(CEXTRA)' 'MV=$(MV)' 'CP=$(CP)'\ 'TAR=$(TAR)' 'MKDIR=$(MKDIR)'; \ cd ../ ;)####install sumasuma_install: ( if [ ! -d $(INSTALLDIR) ]; then $(MKDIR) -p $(INSTALLDIR); echo WARNING: directory $(INSTALLDIR) has been created. ; fi ;\ $(CP) SUMA/suma SUMA/MakeColorMap SUMA/ROI2dataset SUMA/3dVol2Surf \ SUMA/3dSurf2Vol SUMA/SurfMeasures SUMA/SurfFWHM \ SUMA/ScaleToMap SUMA/MapIcosahedron SUMA/CreateIcosahedron \ SUMA/CompareSurfaces \ SUMA/ConvertSurface SUMA/ConvertDset SUMA/SurfClust SUMA/IsoSurface \ SUMA/ConvexHull SUMA/SUMA_glxdino SUMA/SUMA_pixmap2eps SUMA/SurfaceMetrics \ SUMA/inspec SUMA/quickspec SUMA/FSread_annot SUMA/SurfPatch SUMA/SurfQual \ SUMA/SurfSmooth SUMA/SUMA_paperplane \ SUMA/SampBias SUMA/3dSkullStrip SUMA/3dCRUISEtoAFNI \ SUMA/3dBRAIN_VOYAGERtoAFNI SUMA/3dSurfMask \ SUMA/SurfToSurf SUMA/Surf2VolCoord SUMA/ROIgrow SUMA/SurfDsetInfo \ SUMA/SurfInfo SUMA/AnalyzeTrace SUMA/DriveSuma SUMA/SurfDist \ SUMA/SpharmReco SUMA/SpharmDeco SUMA/prompt_user SUMA/SurfRetinoMap \ SUMA/ParseName SUMA/3dGenPriors SUMA/3dSeg SUMA/SurfExtrema SUMA/3dinfill \ SUMA/3dHist \ ${INSTALLDIR} ; \ if [ -f SUMA/SurfMesh ]; then $(CP) SUMA/SurfMesh ${INSTALLDIR} ; fi; \ $(CP) @SUMA_* ${INSTALLDIR} ;) suma: suma_clean suma_exec suma_installsuma_gts: suma_clean suma_exec suma_gts_progs suma_installsuma_fromobjs: suma_link suma_install####R toys#For compiling R programs, you'll need to do the following:# run tcsh ./@RmakeOpts and see that it creates Makefile.R.INCLUDE# add to the end of your Makefile line:# include Makefile.R.INCLUDE# and then: make 3dTsmoothR && mv 3dTsmoothR YOUR_ABIN/#AFNI_embeddedRCall.o: AFNI_embeddedRCall.c $(RM) AFNI_embeddedRCall.o $(CC) $(RccCOMopt) -c AFNI_embeddedRCall.c $(INFLAGS)3dTsmoothR: 3dTsmoothR.c AFNI_embeddedRCall.o $(RM) 3dTsmoothR.o 3dTsmoothR $(CC) $(RccCOMopt) -c 3dTsmoothR.c $(INFLAGS) $(CC) -o 3dTsmoothR 3dTsmoothR.o $(LFLAGS) \ $(LLIBS) $(RccCOMlfl) AFNI_embeddedRCall.otoyR: toyR.c AFNI_embeddedRCall.o $(RM) toyR.o toyR $(CC) $(RccCOMopt) -c toyR.c $(INFLAGS) $(CC) -o toyR toyR.o $(LFLAGS) \ $(LLIBS) $(RccCOMlfl) AFNI_embeddedRCall.o####R_io.so:R_io.c libmri.a ( if which R >/dev/null ; then \ echo PKG_CPPFLAGS = $(INFLAGS) > Makevars ;\ echo PKG_LIBS = $(LFLAGS) $(LLIBS) >> Makevars ;\ R CMD SHLIB R_io.c ; \ else echo WARNING: Cannot build R_io.so because R is not installed;\ fi ; ) |
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