How to install AFNI for nipype

[TheChymera]

Hi, I am currently writing some packages for AFNI/FSL/SPM for my favourite distro (Gentoo).
I plan to use these toolkits via nipype.
On the example of AFNI: I am currently placing everything into /opt/afni:

1dAstrip                  @FindAfniDsetPath
1dBandpass                FIRdesign
1dBport                   @fix_FSsphere
1dcat                     @float_fix
1dCorrelate               float_scan
@1dDiffMag                from3d
1ddot                     @FromRAI
1dDW_Grad_o_Mat           @FSlabel2dset
1deval                    FSread_annot
1dfft                     @FS_roi_label
1dFlagMotion              ftosh
1dGC.R                    @FullPath
1dgenARMA11               funstuff
1dgrayplot                ge_header
1dMarry                   gen_epi_review.py
1dmatcalc                 gen_group_command.py
1dnorm                    gen_ss_review_scripts.py
1dplot                    gen_ss_review_table.py
1dRplot                   @GetAfniBin
1dRplot.R                 @GetAfniDims
1dSEM                     @GetAfniID
1dSEMr.R                  @GetAfniOrient
1dsum                     @GetAfniPrefix
1dSVAR.R                  @GetAfniRes
1dsvd                     @GetAfniView
1d_tool.py                gifti_tool
1dtranspose               @global_parse
1dTsort                   gui_uber_align_test.py
1dUpsample                gui_uber_skel.py
24swap                    gui_uber_subj.py
2dImReg                   gui_uber_ttest.py
@2dwarper                 gui_xmat.py
@2dwarper.Allin           HalloSuma
2perm                     @help.AFNI
2swap                     help_format
3dABoverlap               Ifile
3dAcost                   im2niml
3dAFNIto3D                imand
3dAFNItoANALYZE           imaver
3dAFNItoMINC              imcalc
3dAFNItoNIFTI             imcat
3dAFNItoNIML              imcutup
3dAFNItoRaw               imdump
3dAllineate               immask
3dANALYZEtoAFNI           imreg
3dAnatNudge               imrotate
3dAnhist                  imstack
3danisosmooth             imstat
3dANOVA                   imupsam
3dANOVA2                  inspec
3dANOVA3                  @Install_AfniRetinoDemo
3dAOV.R                   @Install_ClustScat_Demo
3dAttribute               @Install_FATCAT_DEMO
3dAutobox                 @Install_FATMVM_DEMO
3dAutomask                @Install_InstaCorr_Demo
3dAutoTcorrelate          @Install_MEICA_Demo
3daxialize                @Install_RSFMRI_Motion_Group_Demo
3dBandpass                @Install_TSrestMovieDemo
3dBlurInMask              InstaTract
3dBlurToFWHM              @isOblique
3dBRAIN_VOYAGERtoAFNI     @IsoMasks
3dBrickStat               IsoSurface
3dbuc2fim                 killer.h
3dbucket                  Level2.R
3dcalc                    lib_afni1D.py
3dClipLevel               libcoxplot.a
3dclust                   libf2c.a
3dClustCount              lib_fat_funcs.py
3dClustSim                lib_fat_plot_sel.py
3dCM                      lib_fat_Rfactor.py
3dConformist              libGLws.a
3dConvolve                libgts.a
3dcopy                    lib_matplot.py
3dCountSpikes             libmri.a
3dCRUISEtoAFNI            libmrix.a
3ddata.h                  lib_qt_gui.py
3dDeconvolve              lib_realtime.py
3dDeconvolve_f            lib_RR_plot.py
3ddelay                   lib_subjects.py
3dDespike                 libSUMA.a
3dDetrend                 lib_surf_clustsim.py
3dDFT                     lib_system_check.py
3ddot                     lib_textdata.py
3dDTeig                   lib_timing.py
3dDTtoDWI                 lib_uber_align.py
3dDTtoNoisyDWI            lib_uber_skel.py
3ddup                     lib_uber_subject.py
3dDWItoDT                 lib_uber_ttest.py
3dDWUncert                libvolpack.a
3dedge3                   lib_wx.py
3dEigsToDT                list_struct.h
3dEmpty                   lpc_align.py
3dEntropy                 machdep.h
3dErrtsCormat             MakeColorMap
3dExtrema                 @MakeLabelTable
3dFDR                     @make_plug_diff
3dFFT                     make_pq_script.py
3dfim                     make_random_timing.py
3dfim+                    @make_stim_file
3dFourier                 make_stim_times.py
3dfractionize             MapIcosahedron
3dFriedman                map_TrackID
3dFWHM                    mayo_analyze
3dFWHMx                   mcw_glob.h
3dGC.R                    mcw_malloc.h
3dGenFeatureDist          meica.libs
3dGenPriors               meica.py
3dGetrow                  misc_math.h
3dGroupInCorr             model_beta.so
3dHist                    model_constant.so
3dhistog                  model_conv_cosine4.so
3dICA.R                   model_conv_diffgamma.so
3dICC.R                   model_convgamma2a.so
3dICC_REML.R              model_convgamma.so
3dinfill                  model_conv_PRF_6.so
3dinfo                    model_conv_PRF.so
3dIntracranial            model_demri_3.so
3dInvFMRI                 model_diffexp.so
3dkmeans                  model_diffusion.so
3dKruskalWallis           model_expMEMRI3.so
3dKS.R                    model_expMEMRI.so
3dLME                     model_expr2.so
3dLME.R                   model_exp.so
3dLocalBistat             model_gammavar.so
3dLocalHistog             model_linear.so
3dLocalPV                 model_linplusort.so
3dLocalstat               model_michaelis_menton.so
3dLocalSVD                model_null.so
3dLRflip                  model_quadratic.so
3dLSS                     model_sinewave_apf.so
3dMannWhitney             model_sinewave_ap.so
3dmaskave                 model_squarewave_apf.so
3dmaskdump                model_squarewave_ap.so
3dmaskSVD                 model_trnglwave_apf.so
3dMaskToASCII             model_trnglwave_ap.so
3dmask_tool               model_zero.so
3dmatcalc                 module_test_lib.py
3dMatch                   @move.to.series.dirs
3dmatmult                 mpeg_encode
3dMax                     mri_dicom_stuff.h
3dmaxima                  mrilib.h
3dMean                    mritopgm
3dMedianFilter            mri_warpfield.h
3dMEMA                    multivector.h
3dMEMA.R                  mycat
3dmerge                   myget
3dMINCtoAFNI              neuro_deconvolve.py
3dMVM                     nicat
3dMVM.R                   niccc
3dNetCorr                 nifti1.h
3dnewid                   nifti1_io.h
3dNLfim                   nifti1_test
3dnoise                   nifticdf.h
3dNormalityTest           nifti_tool
3dNotes                   niml_feedme
3dnvals                   niml.h
3dNwarpAdjust             niprobe
3dNwarpApply              @NoExt
3dNwarpCalc               @NoisySkullStrip
3dNwarpCat                @NoPound
3dNwarpFuncs              @np
3dNwarpXYZ                nsize
3dOverlap                 option_list.py
3dPAR2AFNI.pl             @parse_afni_name
3dpc                      @parse_name
3dPeriodogram             ParseName
3dPolyfit                 plug_3ddot.so
3dProbTrackID             plug_3Ddump_V2.so
3dproject                 plug_3ddup.so
3dQwarp                   plug_3dsvm.so
3dRank                    plug_4Ddump.so
3dRankizer                plug_afnihistory.so
3drefit                   plug_aslA3D3.so
3dRegAna                  plug_betafit.so
3dReHo                    plug_clust.so
3dREMLfit                 plug_compress.so
3drename                  plug_coorder.so
3dresample                plug_copy.so
3dRetinoPhase             plug_crender.so
3dretroicor               plug_deconvolve.so
3dROIMaker                plug_delay_V2.so
3dROIstats                plug_drawdset.so
3drotate                  plug_edit.so
3dRowFillin               plug_extract.so
3dRprogDemo               plug_fourier.so
3dRprogDemo.R             plug_hemisub.so
3dRSFC                    plug_histog_multi.so
3dSeg                     plug_histog.so
3dSetupGroupInCorr        plug_imreg.so
3dSignatures              plug_L1fit.so
3dSignatures.R            plug_lsqfit.so
3dSkullStrip              plug_maskave.so
3dSpatNorm                plug_maskcalc.so
3dStatClust               plug_maxima.so
3dSurf2Vol                plug_nlfit.so
3dSurfMask                plug_notes.so
3dsvm                     plug_nth_dataset.so
3dSynthesize              plug_nudge.so
3dTagalign                plugout_drive
3dTcat                    plugout_ijk
3dTcorr1D                 plugout_tt
3dTcorrelate              plugout_tta
3dTcorrMap                plug_permtest.so
3dTfitter                 plug_power.so
3dThreetoRGB              plug_realtime.so
3dTnorm                   plug_rename.so
3dTORTOISEtoHere          plug_render.so
3dToutcount               plug_reorder.so
3dToyProg                 plug_retroicor.so
3dTproject                plug_roiedit.so
3dTqual                   plug_roiplot.so
3dTrackID                 plug_scatplot.so
3dTRfix                   plug_second_dataset.so
3dTSgen                   plug_stats.so
3dTshift                  plug_stavg.so
3dTsmooth                 plug_tag.so
3dTsort                   plug_threshold.so
3dTstat                   plug_ttget.so
3dttest                   plug_vol2surf.so
3dttest++                 plug_volreg.so
3dTwotoComplex            plug_wavelets.so
3dUndump                  plug_zeropad.so
3dUnifize                 prompt_user
3dUniformize              @Purify_1D
3dUpsample                python_module_test.py
3dVol2Surf                qdelaunay
3dvolreg                  qhull
3dWarp                    quick.alpha.vals.py
3dWarpDrive               quickspec
3dWavelets                @Quiet_Talkers
3dWilcoxon                quotize
3dWinsor                  @radial_correlate
3dXYZcat                  rbox
3dZcat                    rcmat.h
3dZcutup                  read_matlab_files.py
3dZeropad                 README.3dsvm.realtime
3dZregrid                 README.afnigui
@4Daverage                README.atlas_building
4swap                     README.attributes
abut                      README.bzip2
@AddEdge                  README.changes
adwarp                    README.compression
afni                      README.copyright
AFNI.afnirc               README.driver
AFNI_atlas_spaces.niml    README.environment
afni_base.py              README.func_types
AFNI_Batch_R              README.Ifile
@AfniEnv                  README.notes
afni_environ.h            README.permtest
afnigui_cursor1030.jpg    README.plugouts
afnigui_cursor1100.jpg    README.realtime
afnigui.html              README.registration
afnigui_logo.jpg          README.render_scripts
afni_history              README.roi
AFNIio.R                  README.setup
AFNI_label.h              README.volreg
afni_open                 README.web
@AfniOrient2RAImap        README.ziad
@AfniOrientSign           realtime_receiver.py
AFNIplot.R                @RenamePanga
afni_proc.py              @Reorder
afni_restproc.py          @RetinoProc
@afni.run.me              @R_funclist
afni_run_R                r_idisp.h
afni_skeleton.py          r_misc.h
afni_suma.h               rmz
AFNI.sumarc               r_new_resam_dset.h
afni_system_check.py      ROI2dataset
afni_util.py              @ROI_Corr_Mat
afni_vcheck               ROIgrow
afni_warp.h               rotcom
afni_xmat.py              rPkgsInstall
aiv                       rPkgsInstall.R
@Align_Centers            RSFgen
align_epi_anat.py         rtfeedme
@align_partial_oblique    SampBias
AlphaSim                  ScaleToMap
Amalloc.h                 @ScaleVolume
AnalyzeTrace              @ScriptCheck
@ANATICOR                 serial_helper
Aomp.h                    sfim
apsearch                  @Shift_Volume
ask_me.py                 @ShowDynamicRange
@Atlasize                 siemens_vision
@auto_align               Signatures.R
@auto_tlrc                @simulate_motion
auto_warp.py              slow_surf_clustsim.py
balloon                   smooth.R
@build_afni_Xlib          SpharmDeco
byteorder                 @Spharm.examples
cat_matvec                SpharmReco
ccalc                     sqwave
cdf                       @statauxcode
@Center_Distance          strblast
@CheckForAfniDset         suma
cjpeg                     @SUMA_AlignToExperiment
@clean_help_dir           suma_change_spec
@clip_volume              @SUMA_FSvolToBRIK
column_cat                SUMA_glxdino
@CommandGlobb             @SUMA_Make_Spec_Caret
CompareSurfaces           @SUMA_Make_Spec_FS
@compute_gcor             @SUMA_Make_Spec_SF
ConvertDset               SUMA_paperplane
ConvertSurface            SUMA_pixmap2eps
ConvexHull                Surf2VolCoord
count                     SurfaceMetrics
coxplot.h                 SurfClust
CreateIcosahedron         SurfDist
cs.h                      SurfDsetInfo
cs_qsort_small.h          SurfExtrema
cs_sort_template.h        SurfFWHM
db_mod.py                 SurfInfo
@DeblankFileNames         SurfMeasures
debugtrace.h              SurfMesh
demo.fixed.niml.do        SurfPatch
demo.mobile.niml.do       SurfQual
@demo_prompt              SurfRetinoMap
@DiceMetric               SurfSmooth
dicom_hdr                 @SurfSmooth.HEAT_07.examples
dicom_hinfo               SurfToSurf
dicom_to_raw              @T1scale
Dimon                     tagset.h
Dimon1                    tfim
djpeg                     thd_atlas.h
@DO.examples              thd_compress.h
@DoPerRoi.py              thd_iochan.h
@DriveAfni                thd_maker.h
DriveSuma                 thd_ttatlas_CA_EZ.h
@DriveSuma                thd_ttatlas_query.h
DTIStudioFibertoSegments  @TimeDiff
@DTI_studio_reposition    timing_tool.py
editvol.h                 to3d
eg_main_chrono.py         @toMNI_Awarp
eispack.h                 @toMNI_Qwarpar
@ElectroGrid              @ToRAI
ent16                     uber_align_test.py
@escape-                  uber_proc.py
@ExamineGenFeatDists      uber_skel.py
ExamineXmat               uber_subject.py
ExamineXmat.R             uber_ttest.py
f2c.h                     ui_xmat.py
@fast_roi                 @UpdateAfni
fat_lat_csv.py            @update.afni.binaries
fat_mat_sel.py            vecmat.h
fat_mvm_gridconv.py       Vecwarp
fat_mvm_prep.py           vol2surf.h
fat_mvm_review.py         @VolCenter
fat_mvm_scripter.py       volpack.h
fat_roi_row.py            waver
FD2                       whereami
fdrval                    whirlgif
fftest                    xmat_tool.py
file_tool                 Xphace
fim2                      znzlib.h

should I add the path for all these files to PATH (seems a bit overkill)? Currently I am adding the path to LDPATH only (and adding only afni to /usr/bin - ergo my path) - is that enough?

[satra]

@TheChymera - nipype command line interfaces simply call the executable with proper formatting. so yes it needs to be available in the shell. now you could potentially make the afni class itself take a base directory or prefix that it adds to the command by overwriting the cmdline property.

[TheChymera]

many thanks!