make_bem.sh

#!/bin/csh -ef

# Do recon-all and get flash5 and flash30 files to nii/*.nii:
# mcverter --format nifti -ndo . ${THIS_DIR}/DICOM/
# INRAGE=`find . -name "*MEMPRAGE*.nii"`
# IN5=`find . -name "*FLASH5*.nii"`
# IN30=`find . -name "*FLASH30*.nii"`
# OUTNAME="${PWD##*/}"
# SUBJ_DIR="$SUBJECTS_DIR/$OUTNAME"
# mkdir -p $SUBJ_DIR
# mkdir -p $SUBJ_DIR/mri
# mkdir -p $SUBJ_DIR/mri/orig
# mkdir -p $SUBJ_DIR/nii
# cp $INRAGE $SUBJ_DIR/nii/
# cp $IN5 $SUBJ_DIR/nii/
# cp $IN30 $SUBJ_DIR/nii/
# MYDIR=${PWD}
# echo $INRAGE
# cd $SUBJ_DIR/nii
# ln -s $INRAGE MEMPRAGE.nii
# ln -s $IN5 flash5.nii
# ln -s $IN30 flash30.nii
# cd $MYDIR
# mri_concat --rms --i $INRAGE --o $SUBJECTS_DIR/$OUTNAME/mri/orig/001.mgz
# recon-all -subject $OUTNAME -all

set SUBJECT = `pwd|sed 's:/.*/::'` 
set source_dir = $SUBJECTS_DIR/$SUBJECT/nii
set dest_dir = $SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps

cd $SUBJECTS_DIR/$SUBJECT/mri

mkdir -p flash
cd flash
mkdir -p parameter_maps
mne_setup_mri --mri T1 --subject $SUBJECT --overwrite
cd $dest_dir
mri_convert $source_dir/flash30.nii  ./flash30.mgz
mri_convert $source_dir/flash5.nii  ./flash5.mgz
fsl_rigid_register -r ../../rawavg.mgz -i ./flash30.mgz -o flash30_reg.mgz
fsl_rigid_register -r ../../rawavg.mgz -i ./flash5.mgz -o flash5_reg.mgz
mkdir -p ../../flash30/
mkdir -p ../../flash5/
mri_convert -ot cor ./flash30_reg.mgz ../../flash30
mri_convert -ot cor ./flash5_reg.mgz ../../flash5
cd ../../
mri_convert -ot cor brainmask.mgz brain
mri_convert -ot cor T1.mgz T1

mri_make_bem_surfaces $SUBJECT
mne_watershed_bem --subject $SUBJECT --overwrite

cd ../bem/
mne_convert_surface --tri inner_skull.tri --swap --surfout inner_skull.surf
mne_convert_surface --tri outer_skull.tri --swap --surfout outer_skull.surf
cp ./watershed/${SUBJECT}_outer_skin_surface ./outer_skin.surf
mne_setup_forward_model --surf --ico 4 --subject $SUBJECT
mne_setup_source_space --subject $SUBJECT --overwrite

if( ! -e $SUBJECTS_DIR/$SUBJECT/bem/${SUBJECT}-head-dense.fif ) then 
	echo
	echo Making dense head...
	mkheadsurf -subjid $SUBJECT
	cd $SUBJECTS_DIR/$SUBJECT/bem
	mne_surf2bem --surf ../surf/lh.seghead --id 4 --check --fif ${SUBJECT}-head-dense.fif
	mv ${SUBJECT}-head.fif ${SUBJECT}-head-sparse.fif
else
	rm ${SUBJECT}-head.fif
endif
ln -s ${SUBJECT}-head-dense.fif ${SUBJECT}-head.fif
echo Done.