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" # 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}