{{{ #!/bin/sh # # this is an example of a script that will convert the freeSurfer orig.mgz high resolution, # to a nifti format (anat.nii) that will be readable by spm. This will allow coregistration # of the freeSurfer reference anatomical (anat.nii) to the source image (spm native space # anatomical image) and any other image of your choice (e.g. mean*.nii) ## 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 " converting high resolution T1 image from .mgz to .nii" echo " " echo "=======================================================" cd ${thePath}/${subjects[m]}/mri/ echo "the current directory is `pwd`" mri_convert \ orig.mgz \ anat.nii done # converting .mgz to nifti format }}}