dcm-generate-bms-analysis.sh~

#!/bin/bash

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## DCM-GENERATE-BMS-ANALYSIS.SH
## ---------------------------------------------------------------- ##
## Extract DCMs for the Autism task
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## History 
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##
## 2015-09-27 : Added documentation and help string
##
## 2013-05-16 : File Created
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NL="
"   # new line

HELP_MSG="dcm-generate-bms-analysis
 --------------------------------------
 This program creates a matlab script
 to perform a Bayesian Model Selection
 analysis.
  
 Usage
 --------------------------------------
 $ dcm-generate-bms-analysis.sh 
   <models-file> <DCM dir>
   <subj1> <sub2> ... <subN>
 
 where:
   <models-file>  is a text file listing
          the names of the DCM models
          to compare (including the trailing
          .mat).
   <DCM dir>  is the name of the folder
          where the BMS file will be
          placed.
   <subX>   is the [list of] of subject
          folders.

 Notes
 --------------------------------------
 * The script must be run from the root
   folder, where all the subjects 
   folders are located
 * Each subject folder must have a 'DCM'
   directory where the model is located
 * At least two arguments need to be 
   provided (model and at least one 
   subject)
" 

if [ $# -lt 3 ]; then
    echo "$HELP_MSG"
    exit
fi


models=$1      # Model file name
shift;

dir=`pwd`/$1   # DCM folder name
shift

echo "matlabbatch{1}.spm.stats.bms.bms_dcm.dir = {'${dir}'};"
j=0
for s in $@; do
    j=$((j+1))
    echo "matlabbatch{1}.spm.stats.bms.bms_dcm.sess_dcm{${j}}.mod_dcm = {"
    while read model; do
	model_path=`pwd`/$s/DCM/${model}
	echo "'${model_path}'"
    done < $models
    echo "};"
done
echo "matlabbatch{1}.spm.stats.bms.bms_dcm.model_sp = {''};"
echo "matlabbatch{1}.spm.stats.bms.bms_dcm.load_f = {''};"
echo "matlabbatch{1}.spm.stats.bms.bms_dcm.method = 'FFX';"
echo "matlabbatch{1}.spm.stats.bms.bms_dcm.family_level.family_file = {''};"
echo "matlabbatch{1}.spm.stats.bms.bms_dcm.bma.bma_no = 0;"
echo "matlabbatch{1}.spm.stats.bms.bms_dcm.verify_id = 0;"