reg_epi.sh

#!/bin/bash
#Author: Anne
#Purpose: register t1 to standard space
# Things it does
# 1. skull strip data
# 2. register to standard space
# 3. invert transformation

source globals.sh   
echo "subject number is $subjectNum, day $dayNum, run $runNum"
subject_save_path=$project_path/data/subject$subjectNum/day$dayNum/reg
# move into subjects directory
mkdir -pv $subject_save_path
cd $subject_save_path
echo "moving into folder: $subject_save_path"

echo "subject name is $subjName"
echo "looking for dicoms in $scanFolder"

# Process t1-weighted MPRAGE and check brain extraction!
functionalFN=exfunc
highresFN=highres
fileN=6
exfunc_str=$(printf "%s/001_0000%02d_0000%02d.dcm" "$scanFolder" "$functionalScan" "$fileN")
exfunc2highres_mat=example_func2highres
highres2exfunc_mat=highres2example_func
if [ $1 -eq 1 ]
then
	dcm2niix -f $functionalFN -z y -o $subject_save_path -s y $exfunc_str
fi
if [ $2 -eq 1 ]
then
	# now register to highres!
	exfunc2highres_mat=example_func2highres
	highres2exfunc_mat=highres2example_func
	epi_reg --epi=$functionalFN --t1=$highresFN --t1brain=$highresFN'_'brain --out=$exfunc2highres_mat
	convert_xfm -inverse -omat $highres2exfunc_mat'.'mat $exfunc2highres_mat'.'mat
	# now register mask to all data
	applywarp -i $project_path/$roi_name'.'nii.gz -r $functionalFN'.'nii.gz -o $roi_name'_'exfunc.nii.gz -w standard2highres_warp.nii.gz --postmat=$highres2exfunc_mat'.'mat 
	# check after here that the applied warp is binary and in the right
	# orientation so we could just apply to nifti files afterwards
	
fi
bet $functionalFN'.'nii.gz $functionalFN'_'brain.nii.gz -R -m
fslview $functionalFN'.'nii.gz $functionalFN'_'brain.nii.gz $functionalFN'_'brain_mask.nii.gz $roi_name'_'exfunc.nii.gz &

echo "copying this version of file into subject folder for safe keeping!"
mkdir -pv $project_path/data/subject$subjectNum/usedscripts/
cp $project_path/reg_epi.sh $project_path/data/subject$subjectNum/usedscripts/reg_epi.sh
cd $project_path
echo "done!, moving into project path"