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These are the instructions given to me for installing AFNI, yet when I completed them, it still tells me 'command not found' for the 'afni' command.

sudo yum install libXp tcsh
sudo yum install PyQt4 R   

(This was not correct, but I was able to get it to work with this):

sudo apt-get install libxp6 tcsh
sudo apt-get install python-qt4 r-base

Then:

cd
mkdir abin

Then it says to choose one of these binaries. I wasn't sure which one to choose, but I chose #3:

  1. linux_openmp : for multi-CPU systems, (needs libgomp)
  2. linux_openmp_64 : 64-bit version of the same
  3. linux_xorg7 : otherwise current linux package
  4. linux_xorg7_64 : 64-bit version of the same

Then:

set package = linux_xorg7
wget http://afni.nimh.nih.gov/pub/dist/tgz/$package.tgz
tar xvfz $package.tgz
mv $package/* abin
rmdir $package

and finally, add the AFNI package directory ~/abin to your path:

echo 'set path = ( $path ~/abin )' >> ~/.cshrc

Then it said to log out and log back in so the programs are recognized in the path, and then to try these commands upon login:

afni
suma
uber_subject.py

Only the last one worked. The others said 'command not found'.

What went wrong?

When I do 'echo $path' it shows this:

/usr/lib/lightdm/lightdm /usr/local/sbin /usr/local/bin /usr/sbin /usr/bin /sbin /bin /usr/games /usr/local/games /home/owner/abin /home/owner/abin

The output of ls -l /home/owner/abin is:

-rwxr-xr-x 1 owner owner     2134 Nov 29 21:01 @Install_AfniRetinoDemo
-rwxr-xr-x 1 owner owner     1892 Nov 29 21:01 @Install_FATCAT_DEMO
-rwxr-xr-x 1 owner owner     3465 Nov 29 21:01 @Install_InstaCorr_Demo
-rwxr-xr-x 1 owner owner     1683 Nov 29 21:01 @Install_MEICA_Demo
-rwxr-xr-x 1 owner owner     5269 Nov 29 21:01 @Install_RSFMRI_Motion_Group_Demo
-rwxr-xr-x 1 owner owner     2609 Nov 29 21:01 @Install_TSrestMovieDemo
-rwxr-xr-x 1 owner owner      902 Nov 29 21:01 @isOblique
-rwxr-xr-x 1 owner owner     3864 Nov 29 21:01 @IsoMasks
-rwxr-xr-x 1 owner owner 11329870 Nov 29 21:01 IsoSurface
-rwxr-xr-x 1 owner owner     3521 Nov 29 21:01 killer.h
-rwxr-xr-x 1 owner owner    18132 Nov 29 21:01 Level2.R
-rwxr-xr-x 1 owner owner   101340 Nov 29 21:01 lib_afni1D.py
-rw-r--r-- 1 owner owner   221272 Nov 29 21:01 libcoxplot.a
-rw-r--r-- 1 owner owner   220774 Nov 29 21:01 libf2c.a
-rw-r--r-- 1 owner owner    18582 Nov 29 20:53 libGLws.a
-rw-r--r-- 1 owner owner  1299298 Nov 29 21:00 libgts.a
-rwxr-xr-x 1 owner owner    11671 Nov 29 21:01 lib_matplot.py
-rw-r--r-- 1 owner owner  8400460 Nov 29 21:01 libmri.a
-rw-r--r-- 1 owner owner   750488 Nov 29 21:01 libmrix.a
-rwxr-xr-x 1 owner owner    67662 Nov 29 21:01 lib_qt_gui.py
-rw-r--r-- 1 owner owner    61316 Nov 30 14:40 lib_qt_gui.pyc
-rwxr-xr-x 1 owner owner    17868 Nov 29 21:01 lib_realtime.py
-rwxr-xr-x 1 owner owner     3929 Nov 29 21:01 lib_RR_plot.py
-rwxr-xr-x 1 owner owner    55020 Nov 29 21:01 lib_subjects.py
-rw-r--r-- 1 owner owner    46258 Nov 30 14:40 lib_subjects.pyc
-rw-r--r-- 1 owner owner  7842396 Nov 29 20:57 libSUMA.a
-rwxr-xr-x 1 owner owner    29947 Nov 29 21:01 lib_surf_clustsim.py
-rw-r--r-- 1 owner owner     8194 Nov 29 21:01 lib_system_check.py
-rwxr-xr-x 1 owner owner    10148 Nov 29 21:01 lib_textdata.py
-rw-r--r-- 1 owner owner     9272 Nov 30 14:40 lib_textdata.pyc
-rwxr-xr-x 1 owner owner    33042 Nov 29 21:01 lib_timing.py
-rwxr-xr-x 1 owner owner    31904 Nov 29 21:01 lib_uber_align.py
-rwxr-xr-x 1 owner owner    23453 Nov 29 21:01 lib_uber_skel.py
-rwxr-xr-x 1 owner owner    66434 Nov 29 21:01 lib_uber_subject.py
-rw-r--r-- 1 owner owner    55296 Nov 30 14:40 lib_uber_subject.pyc
-rwxr-xr-x 1 owner owner    23340 Nov 29 21:01 lib_uber_ttest.py
-rw-r--r-- 1 owner owner   258384 Nov 29 21:01 libvolpack.a
-rwxr-xr-x 1 owner owner     4517 Nov 29 21:01 lib_wx.py
-rwxr-xr-x 1 owner owner     2432 Nov 29 21:01 list_struct.h
-rwxr-xr-x 1 owner owner    23775 Nov 29 21:01 lpc_align.py
-rwxr-xr-x 1 owner owner    16378 Nov 29 21:01 machdep.h
-rwxr-xr-x 1 owner owner 11268219 Nov 29 21:01 MakeColorMap
-rwxr-xr-x 1 owner owner    33562 Nov 29 21:01 @MakeLabelTable
-rwxr-xr-x 1 owner owner     8745 Nov 29 21:01 @make_plug_diff
-rwxr-xr-x 1 owner owner     4141 Nov 29 21:01 make_pq_script.py
-rwxr-xr-x 1 owner owner    91329 Nov 29 21:01 make_random_timing.py
-rwxr-xr-x 1 owner owner    15388 Nov 29 21:01 @make_stim_file
-rwxr-xr-x 1 owner owner    11915 Nov 29 21:01 make_stim_times.py
-rwxr-xr-x 1 owner owner 11282021 Nov 29 21:01 MapIcosahedron
-rwxr-xr-x 1 owner owner  3496097 Nov 29 20:52 map_TrackID
-rwxr-xr-x 1 owner owner     9080 Nov 29 20:46 mayo_analyze
-rwxr-xr-x 1 owner owner     3975 Nov 29 21:01 mcw_glob.h
-rwxr-xr-x 1 owner owner     3483 Nov 29 21:01 mcw_malloc.h
drwxr-xr-x 4 owner owner     4096 Nov 29 20:33 meica.libs
-rwxr-xr-x 1 owner owner    26764 Nov 29 20:33 meica.py
-rwxr-xr-x 1 owner owner  1088640 Nov 29 20:33 mgh_wh_template+tlrc.BRIK
-rwxr-xr-x 1 owner owner     3246 Nov 29 20:33 mgh_wh_template+tlrc.HEAD
-rwxr-xr-x 1 owner owner      141 Nov 29 21:01 misc_math.h
-rw-r--r-- 1 owner owner  6244968 Nov 29 20:33 MNI152_1mm_uni+tlrc.BRIK.gz
-rw-r--r-- 1 owner owner     4686 Nov 29 20:33 MNI152_1mm_uni+tlrc.HEAD
-rwxr-xr-x 1 owner owner  1726099 Nov 29 20:33 MNIa_caez_colin27_T1_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     2309 Nov 29 20:33 MNIa_caez_colin27_T1_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner  3657483 Nov 29 20:33 MNIa_caez_gw_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     2658 Nov 29 20:33 MNIa_caez_gw_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   166760 Nov 29 20:33 MNIa_caez_lr_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     2771 Nov 29 20:33 MNIa_caez_lr_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   270372 Nov 29 20:33 MNIa_caez_ml_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    18038 Nov 29 20:33 MNIa_caez_ml_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   238153 Nov 29 20:33 MNIa_caez_mpm_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    11872 Nov 29 20:33 MNIa_caez_mpm_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner  1726099 Nov 29 20:33 MNIa_caez_N27+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     2309 Nov 29 20:33 MNIa_caez_N27+tlrc.HEAD
-rwxr-xr-x 1 owner owner  3240810 Nov 29 20:33 MNIa_caez_pmaps_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    18134 Nov 29 20:33 MNIa_caez_pmaps_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   861626 Nov 29 20:33 MNI_avg152T2+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     4983 Nov 29 20:33 MNI_avg152T2+tlrc.HEAD
-rwxr-xr-x 1 owner owner  1726099 Nov 29 20:33 MNI_caez_N27+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     2764 Nov 29 20:33 MNI_caez_N27+tlrc.HEAD
-rwxr-xr-x 1 owner owner   266078 Nov 29 20:33 MNI_EPI+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     4631 Nov 29 20:33 MNI_EPI+tlrc.HEAD
-rwxr-xr-x 1 owner owner     5545 Nov 29 20:52 model_beta.so
-rwxr-xr-x 1 owner owner     5160 Nov 29 20:52 model_constant.so
-rwxr-xr-x 1 owner owner    13916 Nov 29 20:52 model_conv_cosine4.so
-rwxr-xr-x 1 owner owner    15035 Nov 29 20:52 model_conv_diffgamma.so
-rwxr-xr-x 1 owner owner     8883 Nov 29 20:52 model_convgamma2a.so
-rwxr-xr-x 1 owner owner     8183 Nov 29 20:52 model_convgamma.so
-rwxr-xr-x 1 owner owner    31047 Nov 29 20:52 model_demri_3.so
-rwxr-xr-x 1 owner owner     5416 Nov 29 20:52 model_diffexp.so
-rwxr-xr-x 1 owner owner     5262 Nov 29 20:52 model_diffusion.so
-rwxr-xr-x 1 owner owner     5598 Nov 29 20:52 model_expMEMRI3.so
-rwxr-xr-x 1 owner owner     5309 Nov 29 20:52 model_expMEMRI.so
-rwxr-xr-x 1 owner owner     9428 Nov 29 20:52 model_expr2.so
-rwxr-xr-x 1 owner owner     5248 Nov 29 20:52 model_exp.so
-rwxr-xr-x 1 owner owner     5457 Nov 29 20:52 model_gammavar.so
-rwxr-xr-x 1 owner owner     5346 Nov 29 20:52 model_linear.so
-rwxr-xr-x 1 owner owner     5450 Nov 29 20:52 model_linplusort.so
-rwxr-xr-x 1 owner owner     9364 Nov 29 20:52 model_michaelis_menton.so
-rwxr-xr-x 1 owner owner     5089 Nov 29 20:52 model_null.so
-rwxr-xr-x 1 owner owner     5289 Nov 29 20:52 model_quadratic.so
-rwxr-xr-x 1 owner owner     5686 Nov 29 20:52 model_sinewave_apf.so
-rwxr-xr-x 1 owner owner     5345 Nov 29 20:52 model_sinewave_ap.so
-rwxr-xr-x 1 owner owner     5447 Nov 29 20:52 model_squarewave_apf.so
-rwxr-xr-x 1 owner owner     5382 Nov 29 20:52 model_squarewave_ap.so
-rwxr-xr-x 1 owner owner     5546 Nov 29 20:52 model_trnglwave_apf.so
-rwxr-xr-x 1 owner owner     5485 Nov 29 20:52 model_trnglwave_ap.so
-rwxr-xr-x 1 owner owner     5088 Nov 29 20:52 model_zero.so
-rwxr-xr-x 1 owner owner     8004 Nov 29 21:01 module_test_lib.py
-rw-r--r-- 1 owner owner     6312 Nov 30 14:40 module_test_lib.pyc
-rwxr-xr-x 1 owner owner     4947 Nov 29 21:01 @move.to.series.dirs
-rwxr-xr-x 1 owner owner   206652 Nov 29 20:51 mpeg_encode
-rwxr-xr-x 1 owner owner     6496 Nov 29 21:01 mri_dicom_stuff.h
-rwxr-xr-x 1 owner owner    90294 Nov 29 21:01 mrilib.h
-rwxr-xr-x 1 owner owner  3434886 Nov 29 20:43 mritopgm
-rwxr-xr-x 1 owner owner     2696 Nov 29 21:01 mri_warpfield.h
-rwxr-xr-x 1 owner owner     1986 Nov 29 21:01 multivector.h
-rwxr-xr-x 1 owner owner     6890 Nov 29 20:51 mycat
-rwxr-xr-x 1 owner owner  3434851 Nov 29 20:51 myget
-rwxr-xr-x 1 owner owner    11095 Nov 29 21:01 neuro_deconvolve.py
-rwxr-xr-x 1 owner owner  3435203 Nov 29 20:46 nicat
-rwxr-xr-x 1 owner owner  3439008 Nov 29 20:48 niccc
-rwxr-xr-x 1 owner owner    69232 Nov 29 21:01 nifti1.h
-rwxr-xr-x 1 owner owner    25666 Nov 29 21:01 nifti1_io.h
-rwxr-xr-x 1 owner owner   118029 Nov 29 20:47 nifti1_test
-rwxr-xr-x 1 owner owner     8385 Nov 29 21:01 nifticdf.h
-rwxr-xr-x 1 owner owner   202223 Nov 29 20:46 nifti_tool
-rwxr-xr-x 1 owner owner  3452960 Nov 29 20:48 niml_feedme
-rwxr-xr-x 1 owner owner    49354 Nov 29 21:01 niml.h
-rwxr-xr-x 1 owner owner      797 Nov 29 21:01 @NoExt
-rwxr-xr-x 1 owner owner     7876 Nov 29 21:01 @NoisySkullStrip
-rwxr-xr-x 1 owner owner     1619 Nov 29 21:01 @NoPound
-rwxr-xr-x 1 owner owner     3189 Nov 29 21:01 @np
-rwxr-xr-x 1 owner owner  3434883 Nov 29 20:43 nsize
-rwxr-xr-x 1 owner owner    19944 Nov 29 21:01 option_list.py
-rw-r--r-- 1 owner owner    15044 Nov 30 14:40 option_list.pyc
-rwxr-xr-x 1 owner owner      636 Nov 29 21:01 @parse_afni_name
-rwxr-xr-x 1 owner owner      565 Nov 29 21:01 @parse_name
-rwxr-xr-x 1 owner owner 11253274 Nov 29 21:01 ParseName
-rwxr-xr-x 1 owner owner   317923 Nov 29 20:33 paxinos_elsevier_tissue_lores+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     5076 Nov 29 20:33 paxinos_elsevier_tissue_lores+tlrc.HEAD
-rwxr-xr-x 1 owner owner     9467 Nov 29 20:52 plug_3ddot.so
-rwxr-xr-x 1 owner owner    19628 Nov 29 20:52 plug_3Ddump_V2.so
-rwxr-xr-x 1 owner owner     8459 Nov 29 20:52 plug_3ddup.so
-rwxr-xr-x 1 owner owner   446917 Nov 29 20:53 plug_3dsvm.so
-rwxr-xr-x 1 owner owner    24075 Nov 29 20:52 plug_4Ddump.so
-rwxr-xr-x 1 owner owner    24403 Nov 29 20:52 plug_afnihistory.so
-rwxr-xr-x 1 owner owner    19302 Nov 29 20:53 plug_aslA3D3.so
-rwxr-xr-x 1 owner owner    28239 Nov 29 20:52 plug_betafit.so
-rwxr-xr-x 1 owner owner    13850 Nov 29 20:52 plug_clust.so
-rwxr-xr-x 1 owner owner     6749 Nov 29 20:52 plug_compress.so
-rwxr-xr-x 1 owner owner     8651 Nov 29 20:52 plug_coorder.so
-rwxr-xr-x 1 owner owner    11543 Nov 29 20:52 plug_copy.so
-rwxr-xr-x 1 owner owner   373154 Nov 29 20:53 plug_crender.so
-rwxr-xr-x 1 owner owner    59351 Nov 29 20:52 plug_deconvolve.so
-rwxr-xr-x 1 owner owner    45070 Nov 29 20:53 plug_delay_V2.so
-rwxr-xr-x 1 owner owner   104311 Nov 29 20:52 plug_drawdset.so
-rwxr-xr-x 1 owner owner    28058 Nov 29 20:52 plug_edit.so
-rwxr-xr-x 1 owner owner    20423 Nov 29 20:53 plug_extract.so
-rwxr-xr-x 1 owner owner    16036 Nov 29 20:53 plug_fourier.so
-rwxr-xr-x 1 owner owner     9410 Nov 29 20:53 plug_hemisub.so
-rwxr-xr-x 1 owner owner    18399 Nov 29 20:52 plug_histog_multi.so
-rwxr-xr-x 1 owner owner    32771 Nov 29 20:52 plug_histog.so
-rwxr-xr-x 1 owner owner    13098 Nov 29 20:52 plug_imreg.so
-rwxr-xr-x 1 owner owner    13511 Nov 29 20:52 plug_L1fit.so
-rwxr-xr-x 1 owner owner    20026 Nov 29 20:52 plug_lsqfit.so
-rwxr-xr-x 1 owner owner    17777 Nov 29 20:52 plug_maskave.so
-rwxr-xr-x 1 owner owner    20984 Nov 29 20:53 plug_maskcalc.so
-rwxr-xr-x 1 owner owner    60485 Nov 29 20:53 plug_maxima.so
-rwxr-xr-x 1 owner owner    72383 Nov 29 20:52 plug_nlfit.so
-rwxr-xr-x 1 owner owner    34478 Nov 29 20:52 plug_notes.so
-rwxr-xr-x 1 owner owner    22417 Nov 29 20:52 plug_nth_dataset.so
-rwxr-xr-x 1 owner owner    54029 Nov 29 20:52 plug_nudge.so
-rwxr-xr-x 1 owner owner  3443823 Nov 29 20:47 plugout_drive
-rwxr-xr-x 1 owner owner  3439465 Nov 29 20:44 plugout_ijk
-rwxr-xr-x 1 owner owner  3439492 Nov 29 20:44 plugout_tt
-rwxr-xr-x 1 owner owner  3444047 Nov 29 20:43 plugout_tta
-rwxr-xr-x 1 owner owner    37831 Nov 29 20:53 plug_permtest.so
-rwxr-xr-x 1 owner owner    18348 Nov 29 20:52 plug_power.so
-rwxr-xr-x 1 owner owner   146125 Nov 29 20:52 plug_realtime.so
-rwxr-xr-x 1 owner owner     8869 Nov 29 20:52 plug_rename.so
-rwxr-xr-x 1 owner owner     4273 Nov 29 20:52 plug_render.so
-rwxr-xr-x 1 owner owner    24899 Nov 29 20:53 plug_reorder.so
-rwxr-xr-x 1 owner owner    27546 Nov 29 20:53 plug_retroicor.so
-rwxr-xr-x 1 owner owner   187812 Nov 29 20:53 plug_roiedit.so
-rwxr-xr-x 1 owner owner    15365 Nov 29 20:52 plug_roiplot.so
-rwxr-xr-x 1 owner owner    19929 Nov 29 20:52 plug_scatplot.so
-rwxr-xr-x 1 owner owner    19544 Nov 29 20:52 plug_second_dataset.so
-rwxr-xr-x 1 owner owner     8731 Nov 29 20:52 plug_stats.so
-rwxr-xr-x 1 owner owner    15797 Nov 29 20:53 plug_stavg.so
-rwxr-xr-x 1 owner owner    42441 Nov 29 20:52 plug_tag.so
-rwxr-xr-x 1 owner owner    14919 Nov 29 20:53 plug_threshold.so
-rwxr-xr-x 1 owner owner     4274 Nov 29 20:52 plug_ttget.so
-rwxr-xr-x 1 owner owner    44427 Nov 29 20:53 plug_vol2surf.so
-rwxr-xr-x 1 owner owner    24159 Nov 29 20:52 plug_volreg.so
-rwxr-xr-x 1 owner owner    28108 Nov 29 20:52 plug_wavelets.so
-rwxr-xr-x 1 owner owner    10030 Nov 29 20:52 plug_zeropad.so
-rwxr-xr-x 1 owner owner 11308903 Nov 29 21:01 prompt_user
-rwxr-xr-x 1 owner owner     1783 Nov 29 21:01 @Purify_1D
-rwxr-xr-x 1 owner owner     8289 Nov 29 21:01 python_module_test.py
-rwxr-xr-x 1 owner owner   298646 Nov 29 20:45 qdelaunay
-rwxr-xr-x 1 owner owner   302292 Nov 29 20:45 qhull
-rwxr-xr-x 1 owner owner     1909 Nov 29 21:01 quick.alpha.vals.py
-rwxr-xr-x 1 owner owner 11257559 Nov 29 21:01 quickspec
-rwxr-xr-x 1 owner owner     8523 Nov 29 21:01 @Quiet_Talkers
-rwxr-xr-x 1 owner owner    19607 Nov 29 21:01 @radial_correlate
-rwxr-xr-x 1 owner owner   292354 Nov 29 20:45 rbox
-rwxr-xr-x 1 owner owner     1511 Nov 29 21:01 rcmat.h
-rw-r--r-- 1 owner owner     2402 Nov 29 21:01 README.3dsvm.realtime
-rw-r--r-- 1 owner owner    14096 Nov 29 21:01 README.afnigui
-rw-r--r-- 1 owner owner     6080 Nov 29 21:01 README.atlas_building
-rw-r--r-- 1 owner owner    45863 Nov 29 21:01 README.attributes
-rw-r--r-- 1 owner owner    46932 Nov 29 21:01 README.bzip2
-rwxr-xr-x 1 owner owner     2194 Nov 29 20:33 README.caez_atlas_build
-rw-r--r-- 1 owner owner      476 Nov 29 21:01 README.changes
-rw-r--r-- 1 owner owner     4707 Nov 29 21:01 README.compression
-rw-r--r-- 1 owner owner    25610 Nov 29 21:01 README.copyright
-rw-r--r-- 1 owner owner    30919 Nov 29 21:01 README.driver
-rw-r--r-- 1 owner owner   173673 Nov 29 21:01 README.environment
-rw-r--r-- 1 owner owner     5657 Nov 29 21:01 README.func_types
-rw-r--r-- 1 owner owner      587 Nov 29 21:01 README.Ifile
-rw-r--r-- 1 owner owner     6451 Nov 29 21:01 README.notes
-rw-r--r-- 1 owner owner     1684 Nov 29 21:01 README.permtest
-rw-r--r-- 1 owner owner      553 Nov 29 21:01 README.plugouts
-rw-r--r-- 1 owner owner    18268 Nov 29 21:01 README.realtime
-rw-r--r-- 1 owner owner    31330 Nov 29 21:01 README.registration
-rw-r--r-- 1 owner owner     7415 Nov 29 21:01 README.render_scripts
-rw-r--r-- 1 owner owner     6842 Nov 29 21:01 README.roi
-rw-r--r-- 1 owner owner     9487 Nov 29 21:01 README.setup
-rw-r--r-- 1 owner owner     6113 Nov 29 21:01 README.volreg
-rw-r--r-- 1 owner owner     1649 Nov 29 21:01 README.web
-rw-r--r-- 1 owner owner        0 Nov 29 21:01 README.ziad
-rwxr-xr-x 1 owner owner    22443 Nov 29 21:01 realtime_receiver.py
-rwxr-xr-x 1 owner owner    12487 Nov 29 21:01 @RenamePanga
-rwxr-xr-x 1 owner owner     6826 Nov 29 21:01 @Reorder
-rwxr-xr-x 1 owner owner    69275 Nov 29 21:01 @RetinoProc
-rwxr-xr-x 1 owner owner     1010 Nov 29 21:01 @R_funclist
-rwxr-xr-x 1 owner owner     1161 Nov 29 21:01 r_idisp.h
-rwxr-xr-x 1 owner owner  4891010 Nov 29 20:40 R_io.so
-rwxr-xr-x 1 owner owner      742 Nov 29 21:01 r_misc.h
-rwxr-xr-x 1 owner owner  3434934 Nov 29 20:51 rmz
-rwxr-xr-x 1 owner owner      830 Nov 29 21:01 r_new_resam_dset.h
-rwxr-xr-x 1 owner owner 11261471 Nov 29 21:01 ROI2dataset
-rwxr-xr-x 1 owner owner    16964 Nov 29 21:01 @ROI_Corr_Mat
-rwxr-xr-x 1 owner owner 11318872 Nov 29 21:01 ROIgrow
-rwxr-xr-x 1 owner owner  3473422 Nov 29 20:46 rotcom
-rwxr-xr-x 1 owner owner  3448411 Nov 29 20:44 RSFgen
-rwxr-xr-x 1 owner owner  3446887 Nov 29 20:46 rtfeedme
-rwxr-xr-x 1 owner owner 11261647 Nov 29 21:01 SampBias
-rwxr-xr-x 1 owner owner 11267819 Nov 29 21:01 ScaleToMap
-rwxr-xr-x 1 owner owner    10283 Nov 29 21:01 @ScaleVolume
-rwxr-xr-x 1 owner owner      305 Nov 29 20:33 scan_niml_vals.csh
-rwxr-xr-x 1 owner owner     3813 Nov 29 21:01 @ScriptCheck
-rwxr-xr-x 1 owner owner    28744 Nov 29 20:46 serial_helper
-rwxr-xr-x 1 owner owner  3443924 Nov 29 20:43 sfim
-rwxr-xr-x 1 owner owner     5491 Nov 29 21:01 @Shift_Volume
-rwxr-xr-x 1 owner owner     2943 Nov 29 21:01 @ShowDynamicRange
-rwxr-xr-x 1 owner owner  3439042 Nov 29 20:46 siemens_vision
-rwxr-xr-x 1 owner owner    21966 Nov 29 21:01 Signatures.R
-rwxr-xr-x 1 owner owner    27916 Nov 29 21:01 @simulate_motion
-rwxr-xr-x 1 owner owner    12546 Nov 29 21:01 slow_surf_clustsim.py
-rwxr-xr-x 1 owner owner     1063 Nov 29 21:01 smooth.R
-rwxr-xr-x 1 owner owner 11284079 Nov 29 21:01 SpharmDeco
-rwxr-xr-x 1 owner owner     6649 Nov 29 21:01 @Spharm.examples
-rwxr-xr-x 1 owner owner 11275248 Nov 29 21:01 SpharmReco
-rwxr-xr-x 1 owner owner     7612 Nov 29 20:43 sqwave
-rwxr-xr-x 1 owner owner     1128 Nov 29 21:01 @statauxcode
-rwxr-xr-x 1 owner owner  3439004 Nov 29 20:45 strblast
-rwxr-xr-x 1 owner owner 12036076 Nov 29 21:01 suma
-rwxr-xr-x 1 owner owner    46630 Nov 29 21:01 @SUMA_AlignToExperiment
-rwxr-xr-x 1 owner owner     4454 Nov 29 21:01 suma_change_spec
-rwxr-xr-x 1 owner owner     3663 Nov 29 21:01 @SUMA_FSvolToBRIK
-rwxr-xr-x 1 owner owner    16282 Nov 29 21:01 SUMA_glxdino
-rwxr-xr-x 1 owner owner    30640 Nov 29 21:01 @SUMA_Make_Spec_Caret
-rwxr-xr-x 1 owner owner    43418 Nov 29 21:01 @SUMA_Make_Spec_FS
-rwxr-xr-x 1 owner owner    20693 Nov 29 21:01 @SUMA_Make_Spec_SF
-rwxr-xr-x 1 owner owner  1196794 Nov 29 21:01 SUMA_paperplane
-rwxr-xr-x 1 owner owner    16235 Nov 29 21:01 SUMA_pixmap2eps
-rwxr-xr-x 1 owner owner 11319879 Nov 29 21:01 Surf2VolCoord
-rwxr-xr-x 1 owner owner 11288478 Nov 29 21:01 SurfaceMetrics
-rwxr-xr-x 1 owner owner 11265699 Nov 29 21:01 SurfClust
-rwxr-xr-x 1 owner owner 11260459 Nov 29 21:01 SurfDist
-rwxr-xr-x 1 owner owner 11307483 Nov 29 21:01 SurfDsetInfo
-rwxr-xr-x 1 owner owner 11313913 Nov 29 21:01 SurfExtrema
-rwxr-xr-x 1 owner owner 11325245 Nov 29 21:01 SurfFWHM
-rwxr-xr-x 1 owner owner 11309999 Nov 29 21:01 SurfInfo
-rwxr-xr-x 1 owner owner 11335258 Nov 29 21:01 SurfMeasures
-rwxr-xr-x 1 owner owner 11721032 Nov 29 21:01 SurfMesh
-rwxr-xr-x 1 owner owner 11268881 Nov 29 21:01 SurfPatch
-rwxr-xr-x 1 owner owner 11261872 Nov 29 21:01 SurfQual
-rwxr-xr-x 1 owner owner 11318969 Nov 29 21:01 SurfRetinoMap
-rwxr-xr-x 1 owner owner 11323055 Nov 29 21:01 SurfSmooth
-rwxr-xr-x 1 owner owner    11984 Nov 29 21:01 @SurfSmooth.HEAT_07.examples
-rwxr-xr-x 1 owner owner 11330294 Nov 29 21:01 SurfToSurf
-rwxr-xr-x 1 owner owner    10077 Nov 29 21:01 @T1scale
-rwxr-xr-x 1 owner owner     1938 Nov 29 21:01 tagset.h
-rwxr-xr-x 1 owner owner  3444177 Nov 29 20:43 tfim
-rwxr-xr-x 1 owner owner     6453 Nov 29 21:01 thd_atlas.h
-rwxr-xr-x 1 owner owner     3010 Nov 29 21:01 thd_compress.h
-rwxr-xr-x 1 owner owner     5926 Nov 29 21:01 thd_iochan.h
-rwxr-xr-x 1 owner owner     1678 Nov 29 21:01 thd_maker.h
-rwxr-xr-x 1 owner owner     1052 Nov 29 21:01 thd_ttatlas_CA_EZ.h
-rwxr-xr-x 1 owner owner    28648 Nov 29 21:01 thd_ttatlas_query.h
-rwxr-xr-x 1 owner owner     1106 Nov 29 21:01 @TimeDiff
-rwxr-xr-x 1 owner owner    64032 Nov 29 21:01 timing_tool.py
-rwxr-xr-x 1 owner owner  6070158 Nov 29 20:43 to3d
-rwxr-xr-x 1 owner owner     3729 Nov 29 21:01 @toMNI_Awarp
-rwxr-xr-x 1 owner owner    16674 Nov 29 21:01 @toMNI_Qwarpar
-rwxr-xr-x 1 owner owner     2004 Nov 29 21:01 @ToRAI
-rwxr-xr-x 1 owner owner   377624 Nov 29 20:33 TTatlas+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    40896 Nov 29 20:33 TTatlas+tlrc.HEAD
-rwxr-xr-x 1 owner owner   794290 Nov 29 20:33 TT_avg152T1+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     4932 Nov 29 20:33 TT_avg152T1+tlrc.HEAD
-rwxr-xr-x 1 owner owner   781798 Nov 29 20:33 TT_avg152T2+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     5440 Nov 29 20:33 TT_avg152T2+tlrc.HEAD
-rwxr-xr-x 1 owner owner  1356732 Nov 29 20:33 TT_caez_colin27_T1_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     8799 Nov 29 20:33 TT_caez_colin27_T1_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner  2928274 Nov 29 20:33 TT_caez_gw_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     8473 Nov 29 20:33 TT_caez_gw_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   151399 Nov 29 20:33 TT_caez_lr_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     8585 Nov 29 20:33 TT_caez_lr_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   230450 Nov 29 20:33 TT_caez_ml_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    23852 Nov 29 20:33 TT_caez_ml_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   197143 Nov 29 20:33 TT_caez_mpm_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    17687 Nov 29 20:33 TT_caez_mpm_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner  2953181 Nov 29 20:33 TT_caez_pmaps_18+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    23949 Nov 29 20:33 TT_caez_pmaps_18+tlrc.HEAD
-rwxr-xr-x 1 owner owner   138445 Nov 29 20:33 TT_desai_dd_mpm+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    35035 Nov 29 20:33 TT_desai_dd_mpm+tlrc.HEAD
-rwxr-xr-x 1 owner owner  3519331 Nov 29 20:33 TT_desai_ddpmaps+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner   214682 Nov 29 20:33 TT_desai_ddpmaps+tlrc.HEAD
-rwxr-xr-x 1 owner owner   131991 Nov 29 20:33 TT_desai_dk_mpm+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    21386 Nov 29 20:33 TT_desai_dk_mpm+tlrc.HEAD
-rwxr-xr-x 1 owner owner  2419046 Nov 29 20:33 TT_desai_dkpmaps+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner   128396 Nov 29 20:33 TT_desai_dkpmaps+tlrc.HEAD
-rwxr-xr-x 1 owner owner  1568559 Nov 29 20:33 TT_desai_fspmaps+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner   112365 Nov 29 20:33 TT_desai_fspmaps+tlrc.HEAD
-rwxr-xr-x 1 owner owner   791958 Nov 29 20:33 TT_EPI+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     4897 Nov 29 20:33 TT_EPI+tlrc.HEAD
-rwxr-xr-x 1 owner owner  2184281 Nov 29 20:33 TT_icbm452+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner     8730 Nov 29 20:33 TT_icbm452+tlrc.HEAD
-rwxr-xr-x 1 owner owner   701987 Nov 29 20:33 TT_N27_CA_EZ_MPM+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    12387 Nov 29 20:33 TT_N27_CA_EZ_MPM+tlrc.HEAD
-rwxr-xr-x 1 owner owner   552746 Nov 29 20:33 TT_N27_CA_EZ_PMaps+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    18436 Nov 29 20:33 TT_N27_CA_EZ_PMaps+tlrc.HEAD
-rwxr-xr-x 1 owner owner    59999 Nov 29 20:33 TT_N27_EZ_LR+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    11839 Nov 29 20:33 TT_N27_EZ_LR+tlrc.HEAD
-rwxr-xr-x 1 owner owner   114420 Nov 29 20:33 TT_N27_EZ_ML+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    15625 Nov 29 20:33 TT_N27_EZ_ML+tlrc.HEAD
-rwxr-xr-x 1 owner owner  1353925 Nov 29 20:33 TT_N27+tlrc.BRIK.gz
-rwxr-xr-x 1 owner owner    11447 Nov 29 20:33 TT_N27+tlrc.HEAD
-rwxr-xr-x 1 owner owner     9891 Nov 29 21:01 uber_align_test.py
-rwxr-xr-x 1 owner owner    10798 Nov 29 21:01 uber_proc.py
-rwxr-xr-x 1 owner owner    10002 Nov 29 21:01 uber_skel.py
-rwxr-xr-x 1 owner owner    19585 Nov 29 21:01 uber_subject.py
-rwxr-xr-x 1 owner owner    12252 Nov 29 21:01 uber_ttest.py
-rwxr-xr-x 1 owner owner    45044 Nov 29 21:01 ui_xmat.py
-rw-r--r-- 1 owner owner     4784 Nov 29 20:33 UNC_infant_CustomAtlases.niml
-rwxr-xr-x 1 owner owner     6186 Nov 29 21:01 @UpdateAfni
-rwxr-xr-x 1 owner owner    14894 Nov 29 21:01 @update.afni.binaries
-rwxr-xr-x 1 owner owner    34890 Nov 29 21:01 vecmat.h
-rwxr-xr-x 1 owner owner  3578702 Nov 29 20:45 Vecwarp
-rwxr-xr-x 1 owner owner     6508 Nov 29 21:01 vol2surf.h
-rwxr-xr-x 1 owner owner     3150 Nov 29 21:01 @VolCenter
-rwxr-xr-x 1 owner owner    25376 Nov 29 21:01 volpack.h
-rwxr-xr-x 1 owner owner  3453741 Nov 29 20:43 waver
-rwxr-xr-x 1 owner owner  3912691 Nov 29 20:47 whereami
-rwxr-xr-x 1 owner owner    17987 Nov 29 20:51 whirlgif
-rwxr-xr-x 1 owner owner      453 Nov 29 21:01 xmat_tool.py
-rwxr-xr-x 1 owner owner  5943491 Nov 29 20:51 Xphace
-rwxr-xr-x 1 owner owner     3056 Nov 29 21:01 znzlib.h
ubuntu:~> 

And I don't know if this is all of it. Is it supposed to be this long?

share|improve this question
    
What is the output of ls -l /home/owner/abin? –  Braiam Dec 1 '13 at 1:44

1 Answer 1

They really want to make your life difficult. You must use tcsh to use the program. Type tcsh then write afni and suma. You must do this each time.

set path = ($path /home/owner/abin)

tcsh
afni
suma
share|improve this answer
    
still says command not found –  Sarah Nov 30 '13 at 21:44

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