Hi Peter,
I am sorry to bother you again. I noticed that while I can now change the p value, when I select bi-sided? "yes" and select "apply" and "set" it keeps bi-sided set to "no". I have closed and reopened AFNI but this error persists.

I ran the afni system check, with the output provided below:

psy-bdl-macpro-dsn:3dMVM_noresiduals kathrynj$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.6.0
version: Darwin Kernel Version 15.6.0: Wed Nov 2 20:30:56 PDT 2016; root:xnu-3248.60.11.1.2~2/RELEASE_X86_64
distribution: 10.11.6 x86_64
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/kathrynj/abin/afni
afni version : Precompiled binary macosx_10.7_local: May 26 2017
: AFNI_17.1.07
AFNI_version.txt : AFNI_17.1.07, macosx_10.7_local, May 26 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.3.3 (2017-03-06) -- "Another Canoe"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/kathrynj/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0


testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success

checking for R packages...
rPkgsInstall -pkgs ALL -check : success

checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin:/Users/kathrynj/abin:/Users/kathrynj/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/kathrynj/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.1.11

++ 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, cannot check DYLD_LIBRARY_PATH in cur shell, cheating ...
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace
-- recent OS X, cannot check DYLD_LIBRARY_PATH in shell 'tcsh', cheating ...
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate from 'tcsh'
* shell bash: MISSING login setup file, e.g. .bash_profile
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* consider running: cp /Users/kathrynj/abin/AFNI.afnirc ~/.afnirc
* consider running "suma -update_env" for .sumarc
* insufficient data for AFNI bootcamp
* note: pyqt4 is no longer available via brew
* consider installing gcc under homebrew
* consider installing glib under homebrew
* please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in bash
* please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh