1 files changed, 75 insertions, 97 deletions

diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index 3a88539e9f78..4ea9ad76f60f 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -1,3 +1,5 @@
+bin/1dMarry
+bin/1dSEM
 bin/1dcat
 bin/1ddot
 bin/1deval
@@ -22,6 +24,8 @@ bin/3dANALYZEtoAFNI
 bin/3dANOVA
 bin/3dANOVA2
 bin/3dANOVA3
+bin/3dAcost
+bin/3dAllineate
 bin/3dAnatNudge
 bin/3dAnhist
 bin/3dAttribute
@@ -29,21 +33,25 @@ bin/3dAutoTcorrelate
 bin/3dAutobox
 bin/3dAutomask
 bin/3dBRAIN_VOYAGERtoAFNI
+bin/3dBlurToFWHM
 bin/3dBrickStat
 bin/3dCM
 bin/3dCRUISEtoAFNI
 bin/3dClipLevel
 bin/3dConvolve
+bin/3dDFT
 bin/3dDTeig
 bin/3dDWItoDT
 bin/3dDeconvolve
 bin/3dDeconvolve_f
 bin/3dDespike
 bin/3dDetrend
+bin/3dEmpty
 bin/3dEntropy
 bin/3dExtrema
 bin/3dFDR
 bin/3dFWHM
+bin/3dFWHMx
 bin/3dFourier
 bin/3dFriedman
 bin/3dGetrow
@@ -51,9 +59,11 @@ bin/3dIntracranial
 bin/3dInvFMRI
 bin/3dKruskalWallis
 bin/3dLRflip
+bin/3dLocalBistat
 bin/3dLocalstat
 bin/3dMINCtoAFNI
 bin/3dMannWhitney
+bin/3dMax
 bin/3dMean
 bin/3dMedianFilter
 bin/3dNLfim
@@ -67,6 +77,7 @@ bin/3dSpatNorm
 bin/3dStatClust
 bin/3dSurf2Vol
 bin/3dSurfMask
+bin/3dSynthesize
 bin/3dTSgen
 bin/3dTagalign
 bin/3dTcat
@@ -124,6 +135,44 @@ bin/3drotate
 bin/3dttest
 bin/3dvolreg
 bin/4swap
+bin/@2dwarper
+bin/@4Daverage
+bin/@AfniOrient2RAImap
+bin/@AfniOrientSign
+bin/@Align_Centers
+bin/@Center_Distance
+bin/@CheckForAfniDset
+bin/@CommandGlobb
+bin/@DTI_studio_reposition
+bin/@DoPerRoi.py
+bin/@FindAfniDsetPath
+bin/@FromRAI
+bin/@GetAfniID
+bin/@GetAfniOrient
+bin/@GetAfniPrefix
+bin/@GetAfniView
+bin/@IsoMasks
+bin/@NoExt
+bin/@Purify_1D
+bin/@RenamePanga
+bin/@SUMA_AlignToExperiment
+bin/@SUMA_Make_Spec_Caret
+bin/@SUMA_Make_Spec_FS
+bin/@SUMA_Make_Spec_SF
+bin/@ToRAI
+bin/@UpdateAfni
+bin/@VolCenter
+bin/@align_partial_oblique
+bin/@auto_align
+bin/@auto_tlrc
+bin/@clip_volume
+bin/@escape-
+bin/@fix_FSsphere
+bin/@float_fix
+bin/@make_stim_file
+bin/@np
+bin/@parse_afni_name
+bin/@parse_name
 bin/AlphaSim
 bin/AnalyzeTrace
 bin/CompareSurfaces
@@ -133,6 +182,7 @@ bin/ConvexHull
 bin/CreateIcosahedron
 bin/DTIStudioFibertoSegments
 bin/Dimon
+bin/DriveSuma
 bin/FD2
 bin/FSread_annot
 bin/Ifile
@@ -150,6 +200,7 @@ bin/SampBias
 bin/ScaleToMap
 bin/SurfClust
 bin/SurfDsetInfo
+bin/SurfInfo
 bin/SurfMeasures
 bin/SurfPatch
 bin/SurfQual
@@ -161,13 +212,18 @@ bin/Xphace
 bin/abut
 bin/adwarp
 bin/afni
+bin/afni_base.py
+bin/afni_proc.py
+bin/afni_util.py
 bin/afni_vcheck
 bin/aiv
+bin/ask_me.py
 bin/byteorder
 bin/cat_matvec
 bin/ccalc
 bin/cdf
 bin/count
+bin/db_mod.py
 bin/dicom_hdr
 bin/dicom_to_raw
 bin/ent16
@@ -182,6 +238,7 @@ bin/im2niml
 bin/imand
 bin/imaver
 bin/imcalc
+bin/imcat
 bin/imcutup
 bin/imdump
 bin/immask
@@ -191,14 +248,15 @@ bin/imstack
 bin/imstat
 bin/imupsam
 bin/inspec
+bin/make_stim_times.py
 bin/mayo_analyze
-bin/mpegtoppm
 bin/mritopgm
 bin/myget
 bin/nicat
 bin/nifti1_test
 bin/nifti_tool
 bin/nsize
+bin/option_list.py
 bin/p2t
 bin/plugout_drive
 bin/plugout_ijk
@@ -215,6 +273,7 @@ bin/siemens_vision
 bin/sqwave
 bin/strblast
 bin/suma
+bin/suma_change_spec
 bin/tfim
 bin/to3d
 bin/waver
@@ -252,6 +311,7 @@ lib/afni/model_beta.so
 lib/afni/model_constant.so
 lib/afni/model_convgamma.so
 lib/afni/model_convgamma2a.so
+lib/afni/model_demri_3.so
 lib/afni/model_diffexp.so
 lib/afni/model_diffusion.so
 lib/afni/model_gammavar.so
@@ -266,6 +326,7 @@ lib/afni/model_squarewave_ap.so
 lib/afni/model_squarewave_apf.so
 lib/afni/model_trnglwave_ap.so
 lib/afni/model_trnglwave_apf.so
+lib/afni/model_zero.so
 lib/afni/plug_3Ddump_V2.so
 lib/afni/plug_3ddot.so
 lib/afni/plug_3ddup.so
@@ -314,6 +375,8 @@ lib/afni/plug_vol2surf.so
 lib/afni/plug_volreg.so
 lib/afni/plug_wavelets.so
 lib/afni/plug_zeropad.so
+%%DATADIR%%/AFNI.afnirc
+%%DATADIR%%/AFNI.sumarc
 %%DATADIR%%/Dist_Stamp
 %%DATADIR%%/Readme_dist
 %%DATADIR%%/TT_N27+tlrc.BRIK.gz
@@ -328,11 +391,6 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/TT_N27_EZ_ML+tlrc.HEAD
 %%DATADIR%%/TTatlas+tlrc.BRIK.gz
 %%DATADIR%%/TTatlas+tlrc.HEAD
-%%DATADIR%%/face_erinskinner.jpg
-%%DATADIR%%/face_hang_joon_jo.jpg
-%%DATADIR%%/face_melissah.jpg
-%%DATADIR%%/face_sumabucks.jpg
-%%DATADIR%%/splash_sscc2006.jpg
 %%DATADIR%%/face_JimEliassen.jpg
 %%DATADIR%%/face_JohannaBaas.jpg
 %%DATADIR%%/face_SalloumJB.jpg
@@ -342,6 +400,7 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/face_afniman.jpg
 %%DATADIR%%/face_agoldman.jpg
 %%DATADIR%%/face_ahammett.jpg
+%%DATADIR%%/face_alexandrakofinis.jpg
 %%DATADIR%%/face_anewmanetal.jpg
 %%DATADIR%%/face_anugent.jpg
 %%DATADIR%%/face_asanders.jpg
@@ -366,9 +425,11 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/face_cscholl.jpg
 %%DATADIR%%/face_csenior.jpg
 %%DATADIR%%/face_cwettig.jpg
+%%DATADIR%%/face_daveperlman.jpg
 %%DATADIR%%/face_dglen.jpg
 %%DATADIR%%/face_einstein.jpg
 %%DATADIR%%/face_eli.jpg
+%%DATADIR%%/face_erinskinner.jpg
 %%DATADIR%%/face_ernv.jpg
 %%DATADIR%%/face_eteoh.jpg
 %%DATADIR%%/face_faustalui.jpg
@@ -379,6 +440,9 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/face_ggiulietti.jpg
 %%DATADIR%%/face_glarkin.jpg
 %%DATADIR%%/face_grant.jpg
+%%DATADIR%%/face_guidon.jpg
+%%DATADIR%%/face_hamepark.jpg
+%%DATADIR%%/face_hang_joon_jo.jpg
 %%DATADIR%%/face_hanlon.jpg
 %%DATADIR%%/face_heekeren.jpg
 %%DATADIR%%/face_hoffmangobbini.jpg
@@ -417,6 +481,7 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/face_mbeauchamp.jpg
 %%DATADIR%%/face_mbelmonte.jpg
 %%DATADIR%%/face_megcrew.jpg
+%%DATADIR%%/face_melissah.jpg
 %%DATADIR%%/face_mgarolera.jpg
 %%DATADIR%%/face_mkenney.jpg
 %%DATADIR%%/face_mmaieron.jpg
@@ -450,12 +515,15 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/face_sjapee.jpg
 %%DATADIR%%/face_skammy.jpg
 %%DATADIR%%/face_skapdoskar.jpg
+%%DATADIR%%/face_sknoonan.jpg
 %%DATADIR%%/face_smarrett.jpg
 %%DATADIR%%/face_ssaad.jpg
 %%DATADIR%%/face_ssmall.jpg
 %%DATADIR%%/face_steverao.jpg
+%%DATADIR%%/face_sumabucks.jpg
 %%DATADIR%%/face_tieshan.jpg
 %%DATADIR%%/face_tolkien.jpg
+%%DATADIR%%/face_vdcosta.jpg
 %%DATADIR%%/face_vhradil.jpg
 %%DATADIR%%/face_vincent1.jpg
 %%DATADIR%%/face_vincent2.jpg
@@ -491,63 +559,8 @@ lib/afni/plug_zeropad.so
 %%DATADIR%%/splash_marsalbor.jpg
 %%DATADIR%%/splash_mcw03.jpg
 %%DATADIR%%/splash_sscc03.jpg
+%%DATADIR%%/splash_sscc2006.jpg
 %%DATADIR%%/splash_vincent.jpg
-%%PORTDOCS%%%%DOCSDIR%%/1dplot.ps
-%%PORTDOCS%%%%DOCSDIR%%/24swap.ps
-%%PORTDOCS%%%%DOCSDIR%%/2dImReg.ps
-%%PORTDOCS%%%%DOCSDIR%%/2swap.ps
-%%PORTDOCS%%%%DOCSDIR%%/3T_toafni.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dANOVA.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dANOVA2.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dANOVA3.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dDeconvolve.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dExtrema.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dFDR.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dFWHM.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dFriedman.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dIntracranial.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dKruskalWallis.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dMannWhitney.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dNLfim.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dRegAna.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dStatClust.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dTSgen.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dTcat.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dTsmooth.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dWavelets.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dWilcoxon.ps
-%%PORTDOCS%%%%DOCSDIR%%/3daxialize.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dbuc2fim.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dbucket.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dcalc.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dclust.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dcolon.ps
-%%PORTDOCS%%%%DOCSDIR%%/3ddup.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dfim+.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dfim.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dfractionize.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dhistog.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dinfo.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dmaskave.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dmerge.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dnewid.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dnoise.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dnvals.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dpc.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dproject.ps
-%%PORTDOCS%%%%DOCSDIR%%/3drefit.ps
-%%PORTDOCS%%%%DOCSDIR%%/3drotate.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dttest.ps
-%%PORTDOCS%%%%DOCSDIR%%/3dvolreg.ps
-%%PORTDOCS%%%%DOCSDIR%%/4swap.ps
-%%PORTDOCS%%%%DOCSDIR%%/AFNI.changes.cox
-%%PORTDOCS%%%%DOCSDIR%%/AFNI.changes.rhammett
-%%PORTDOCS%%%%DOCSDIR%%/AFNI.changes.rickr
-%%PORTDOCS%%%%DOCSDIR%%/AlphaSim.ps
-%%PORTDOCS%%%%DOCSDIR%%/AlphaSim_fig.ps
-%%PORTDOCS%%%%DOCSDIR%%/FD2.ps
-%%PORTDOCS%%%%DOCSDIR%%/Nonparametric.ps
-%%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/README.Ifile
 %%PORTDOCS%%%%DOCSDIR%%/README.attributes
 %%PORTDOCS%%%%DOCSDIR%%/README.bzip2
@@ -568,41 +581,6 @@ lib/afni/plug_zeropad.so
 %%PORTDOCS%%%%DOCSDIR%%/README.volreg
 %%PORTDOCS%%%%DOCSDIR%%/README.web
 %%PORTDOCS%%%%DOCSDIR%%/README.ziad
-%%PORTDOCS%%%%DOCSDIR%%/RSFgen.ps
-%%PORTDOCS%%%%DOCSDIR%%/Table.ps
-%%PORTDOCS%%%%DOCSDIR%%/abut.ps
-%%PORTDOCS%%%%DOCSDIR%%/adwarp.ps
-%%PORTDOCS%%%%DOCSDIR%%/afni200.ps
-%%PORTDOCS%%%%DOCSDIR%%/afni_aux.ps
-%%PORTDOCS%%%%DOCSDIR%%/afni_plugins.ps
-%%PORTDOCS%%%%DOCSDIR%%/afni_register.ps
-%%PORTDOCS%%%%DOCSDIR%%/buckets.ps
-%%PORTDOCS%%%%DOCSDIR%%/byteorder.ps
-%%PORTDOCS%%%%DOCSDIR%%/ccalc.ps
-%%PORTDOCS%%%%DOCSDIR%%/cdf.ps
-%%PORTDOCS%%%%DOCSDIR%%/count.ps
-%%PORTDOCS%%%%DOCSDIR%%/fim2.ps
-%%PORTDOCS%%%%DOCSDIR%%/float_scan.ps
-%%PORTDOCS%%%%DOCSDIR%%/from3d.ps
-%%PORTDOCS%%%%DOCSDIR%%/ftosh.ps
-%%PORTDOCS%%%%DOCSDIR%%/imand.ps
-%%PORTDOCS%%%%DOCSDIR%%/imaver.ps
-%%PORTDOCS%%%%DOCSDIR%%/imcalc.ps
-%%PORTDOCS%%%%DOCSDIR%%/imdump.ps
-%%PORTDOCS%%%%DOCSDIR%%/immask.ps
-%%PORTDOCS%%%%DOCSDIR%%/imreg.ps
-%%PORTDOCS%%%%DOCSDIR%%/imrotate.ps
-%%PORTDOCS%%%%DOCSDIR%%/imstack.ps
-%%PORTDOCS%%%%DOCSDIR%%/imstat.ps
-%%PORTDOCS%%%%DOCSDIR%%/imupsam.ps
-%%PORTDOCS%%%%DOCSDIR%%/mritopgm.ps
-%%PORTDOCS%%%%DOCSDIR%%/nsize.ps
-%%PORTDOCS%%%%DOCSDIR%%/p2t.ps
-%%PORTDOCS%%%%DOCSDIR%%/sfim.ps
-%%PORTDOCS%%%%DOCSDIR%%/sqwave.ps
-%%PORTDOCS%%%%DOCSDIR%%/tfim.ps
-%%PORTDOCS%%%%DOCSDIR%%/to3d.ps
-%%PORTDOCS%%%%DOCSDIR%%/waver.ps
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
 @dirrm %%DATADIR%%
 @dirrm lib/afni