{{{ #!/bin/sh # # edit to your needs and save as batchcreateRegistrationFiles.csh in your favorite path location and run # > sh batchcreateRegistrationFiles.csh ## variables ## Freesurfer directory thePath='/imaging/yourusername/yourproject/subjects' subjects=( 'CBUXXXXXX' \ 'CBUYYYYYY' \ ) ## Processing: nsubjects=${#subjects[*]} lastsubj=`expr $nsubjects - 1` 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 mri_info ${thePath}/${subjects[m]}/whereMySPMfilesAre/mean*.nii --vox2ras-tkr --o v2r.dat done # subjects }}}