How to install AFNI for nipype #1067
Description
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?