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fy_web_prep.bash
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fy_web_prep.bash
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#!/bin/bash
echo "FYBORG3000 (c) FNNDSC, BCH 2013"
if [ -z "$3" ]
then
echo "USAGE: `basename $0` {FREESURFER_DIR} {DIFFUSION_DICOM_DIR} {OUTPUT_DIR} [-v]"
exit 1
fi
FREESURFER_DIR=$1
DIFFUSION_DICOM_DIR=$2
OUTPUT_DIR=$3
VERBOSE='-v'
if [ -z "$4" ]
then
VERBOSE=''
fi
#
# GRAB STUFF FROM THE FREESURFER DIR
#
./fy_cherrypick_freesurfer.py -i $FREESURFER_DIR -o $OUTPUT_DIR $VERBOSE
#
# RUN DTI PREP
#
./fy_prep.py -i $DIFFUSION_DICOM_DIR -o $OUTPUT_DIR $VERBOSE
#
# REGISTER DIFFUSION TO T1
#
DIFFUSION_FILE=$OUTPUT_DIR/diffusion.nii.gz
BRAIN_FILE=$OUTPUT_DIR/brain.nii.gz
SEGMENTATION_FILE=$OUTPUT_DIR/aparc+aseg.nii.gz
./fy_register.py -i $DIFFUSION_FILE -i2 $SEGMENTATION_FILE -t $BRAIN_FILE -o $OUTPUT_DIR $VERBOSE
#
# RECONSTRUCT STREAMLINES
#
WARPED_SEGMENTATION_FILE=$OUTPUT_DIR/aparc+aseg_to_diffusion.nii.gz
./fy_reconstruct.py -i $DIFFUSION_FILE -m $WARPED_SEGMENTATION_FILE -o $OUTPUT_DIR $VERBOSE
#
# WARP STREAMLINES
#
FIBERS_FILE=$OUTPUT_DIR/fibers.trk
MATRIX_FILE=$OUTPUT_DIR/diffusion_to_brain.mat
FIBERS_TO_BRAIN_FILE=$OUTPUT_DIR/fibers_to_brain.trk
./fy_warptracks.py -i $FIBERS_FILE -d $DIFFUSION_FILE -b $BRAIN_FILE -m $MATRIX_FILE -o $FIBERS_TO_BRAIN_FILE $VERBOSE
echo 'ALL DONE FOR FY_WEB.PY!'