<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>FreesurferGoodies/batchcreateRegistrationFiles</title><revhistory><revision><revnumber>3</revnumber><date>2013-03-07 21:24:03</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>2</revnumber><date>2012-03-07 15:18:39</date><authorinitials>IanCharest</authorinitials></revision><revision><revnumber>1</revnumber><date>2012-03-07 15:14:40</date><authorinitials>IanCharest</authorinitials></revision></revhistory></articleinfo><screen><![CDATA[#
# edit to your needs and save as batchcreateRegistrationFiles.csh in your favorite path location and run
# > sh batchcreateRegistrationFiles.csh
]]><![CDATA[
## variables
]]><![CDATA[
## Freesurfer directory
thePath='/imaging/yourusername/yourproject/subjects'
]]><![CDATA[
subjects=(
'CBUXXXXXX' \  
'CBUYYYYYY' \ 
)
]]><![CDATA[
## Processing:
]]><![CDATA[
nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`
]]><![CDATA[
for m in `seq 0 ${lastsubj}`
do
        echo "======================================================="
        echo " "
        echo " Creating register.dat and v2r.dat files"
        echo " "
        echo "======================================================="
        
cd ${thePath}/${subjects[m]}/whereMySPMfilesAre
echo "the current directory is `pwd`"
tkregister2 \
 --mov ${thePath}/${subjects[m]}/whereMySPMfilesAre/mean*.nii \
 --s ${subjects[m]} \
 --regheader \
 --noedit \
 --reg register.dat 
]]><![CDATA[
mri_info ${thePath}/${subjects[m]}/whereMySPMfilesAre/mean*.nii --vox2ras-tkr --o v2r.dat
done # subjects]]></screen></article>