Thank you so much for your help, I am using a mac.
Here is one example of a command and output (fMRIdata is an external hard drive plugged into my laptop at the moment, but I get the same output when I try to change directories into "Documents" or something else that is on my physical laptop):
cd fMRIdata
-bash: cd: fMRIdata: No such file or directory
Here is the output of "pwd"
/Users/nikkistuart
Here is the output for "afni_system_check.py -check_all"
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.5.0
version: Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64
distribution: 10.14.4 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/nikkistuart/abin/afni
afni version : Precompiled binary macos_10.12_local: May 10 2019
: AFNI_19.1.08 'Caligula'
AFNI_version.txt : AFNI_19.1.08, macos_10.12_local, May 10 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) -- "Single Candle"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/nikkistuart/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
-------------------------------- env vars --------------------------------
PATH = /Library/Frameworks/Python.framework/Versions/3.7/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/nikkistuart/abin:/Users/nikkistuart/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...9 [ptaylor]: added FT_analysis/results.QC_FT.05 tree
data dir : found AFNI_demos under $HOME
top history: 22 Apr 2019 [rickr]: added AFNI_pamenc
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/nikkistuart/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.2
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
-- consider installing glib under homebrew
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'bash'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
