From 9e4025b22df1b27036d9eaf6500458b742961ca1 Mon Sep 17 00:00:00 2001
From: Daniel A Kessler <kesslerd@umich.edu>
Date: Mon, 16 Jul 2012 14:56:09 -0400
Subject: [PATCH 1/2] Made localization changes to spm8Batch. End users should
 no longer need to make any localization tweaks aside from manually sourcing
 spm8Setup or configuring spm8Setup to be automatically sourced for all or
 some users

---
 spm8Batch/spm8Batch_Global | 13 ++++++++-----
 spm8Batch/spm8Setup        |  3 ++-
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/spm8Batch/spm8Batch_Global b/spm8Batch/spm8Batch_Global
index 99e1cf0d..3b09415d 100755
--- a/spm8Batch/spm8Batch_Global
+++ b/spm8Batch/spm8Batch_Global
@@ -38,15 +38,18 @@ then
 # SOME GLOBAL THINGS TO CHANGE ACCORDING TO SITE
 #    
 
-    topDIR=/Users/rcwelsh/Software
+
+    curdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+    topDIR="$( cd $curdir/.. && pwd )"
     
 # You must point to SPM8 !!!
     
-    SPM8B1=${topDIR}/SPM8/spm8_with_R4667
+    SPM8B1=${topDIR}/SPM/SPM8/spm8_with_R4667
+
     
 # This is Robert Welsh's UNIX batch interface to spm8
     
-    SPM8B2=${topDIR}/spm8Batch/spm8Batch_VBM8
+    SPM8B2=${topDIR}/spm8Batch
     
 # This must point to the place where the SPM8 patch is locally. 
     
@@ -78,7 +81,7 @@ then
 # Mail job will be sent to your user name at the institutionname
 # Please set the instituion email server name here.
     
-    MAILRECPT=med.umich.edu
+    MAILRECPT=umich.edu
     
 #
 # Default email address to send messages to, on the linux machines
@@ -100,7 +103,7 @@ then
     
 # And finally, you need to point to matlab
         
-    MATLAB=/Applications/MATLAB_R2011b.app/bin/matlab
+    MATLAB=`which matlab`
 
 #    
 # Only allow author to execute code during switch.
diff --git a/spm8Batch/spm8Setup b/spm8Batch/spm8Setup
index 34a6b23e..3dcfa109 100755
--- a/spm8Batch/spm8Setup
+++ b/spm8Batch/spm8Setup
@@ -1,2 +1,3 @@
+curdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
-export PATH=/net/dysthymia/spm8Batch:${PATH}
+export PATH=${curdir}:${PATH}

From 113665b12909f640b55c1edf5fe03288c1579381 Mon Sep 17 00:00:00 2001
From: Daniel A Kessler <kesslerd@umich.edu>
Date: Mon, 16 Jul 2012 15:02:09 -0400
Subject: [PATCH 2/2] updated documentation in installation readme of spm8Batch
 to cover new, much more limited installation requirements

---
 spm8Batch/INSTALL_README.txt | 24 ++++++++----------------
 1 file changed, 8 insertions(+), 16 deletions(-)

diff --git a/spm8Batch/INSTALL_README.txt b/spm8Batch/INSTALL_README.txt
index fe02e2f9..edb5f16f 100644
--- a/spm8Batch/INSTALL_README.txt
+++ b/spm8Batch/INSTALL_README.txt
@@ -1,6 +1,6 @@
 # # # # # # # # # # # # # # # # # #
 #
-# This is the spm8Batch processing system written by Robert C. Welsh, Ann Arbor MI
+# This is a modified version of the spm8Batch processing system written by Robert C. Welsh, Ann Arbor MI
 #
 # Copyright 2002-2012
 #
@@ -29,29 +29,21 @@
 #
 # INSTALLATION INSTRUCTIONS:
 #
-# Move the spm8Batch tar distribution file to the directory where you wish the code to 
-# reside. Then untar using
-# 
-# tar -xvf [tarfile]
 #
-# Next you will need to adjust your PATH environmental variable to include 
+# You will need to adjust your PATH environmental variable to include
 # the spm8Batch distribution
 #
-# For bash you can add this to your .bashrc or .bash_profile
-#
-#     export PATH=[spm8Batch_distribution_location]:${PATH}
-#
-# On tcsh you can add this to your .cshrc file.
+# You can do this on the fly by running "source spm8Setup" while in this directory.
+# You can also edit your .bashrc, .bash_profile, or /etc/bashrc startup scripts to source this automatically
+# for all or just some users.
 #
-#     setenv PATH [spm8Batch_distribution_location]:${PATH}
 # 
-# Next you need to implement the localization changes in spm8Batch_Global that are
-# described below. Remember the native language of the spm8Batch system is bash. An
+# Remember the native language of the spm8Batch system is bash. An
 # excellent site for BASH help is:
 # 
 #     http://tldp.org/LDP/abs/html/
 #
-# You will need to have spm8 distribution
+# You will need to have spm8 distribution (Included in this distribution)
 # 
 # You will need to have fsl, at least 4.1.7, it's known to work with 4.1.7 and 4.1.8
 #
@@ -73,7 +65,7 @@
 # -----------------------------------------------------------------
 # -----------------------------------------------------------------
 #
-# LOCALIZATION
+# LOCALIZATION (No longer needs to be edited. This section retained for developer documentation)
 #
 # The only file that has to be modified for local distrubution is the scripts "spm8Batch_Global"
 #