WarpPD25toDeep7t

warpPD25toDeep7t.sh

#!/bin/bash

ANTSPATH="/opt/ANTSGit/bin/"
DIR_TEMPLATE_DEEPBRAIN7T="/home/andreas/AutoPaCEREval/templates/deepbrain7t"
DIR_TEMPLATE_PD25="/home/andreas/AutoPaCEREval/templates/PD25"

DIR_OUTPUT="output"
DIR_OUTPUT_RAW=$DIR_OUTPUT"/raw"
DIR_OUTPUT_SUBJECT_MNI=$DIR_OUTPUT"/subjectMni"
DIR_OUTPUT_DEEPBRAIN7T=$DIR_OUTPUT"/deepbrain7t"
DIR_OUTPUT_TRANSFORMS=$DIR_OUTPUT"/transforms/"

TEMPLATE_LABELS_PD25=$DIR_TEMPLATE_PD25"/PD25-midbrain-0.3mm.nii.gz"
TEMPLATE_LABELS_DEEP7T=${DIR_TEMPLATE_DEEPBRAIN7T}"/labels/t2_hires/deepBrainNuclei/aseg_deepBrainNuclei.nii.gz"
TEMPLATE_LABELS_PD25_IN_DEEP7T=${DIR_TEMPLATE_DEEPBRAIN7T}"/labels/PD25-midbrain-0.3mm-deep7t.nii.gz"

echo "* Warping atlas labels to deep7t *" # impute rigid transform determined before
if [ ! -f $TEMPLATE_LABELS_PD25_IN_DEEP7T ]; then
${ANTSPATH}antsApplyTransforms --default-value 0 --dimensionality 3 \
 --input $TEMPLATE_LABELS_PD25 \
 --interpolation GenericLabel \
 --output $TEMPLATE_LABELS_PD25_IN_DEEP7 \
 --reference-image $TEMPLATE_DEEP7T \
 --transform $DIR_OUTPUT_TRANSFORMS"trans_syn_t2_to_deepbrain7t1Warp.nii.gz" \# {->deep7t_syn}
 --transform [$DIR_OUTPUT_TRANSFORMS"trans_syn_t2_to_deepbrain7t0GenericAffine.mat",0] \# {T2->deep7t_affine}
 --transform [$DIR_OUTPUT_TRANSFORMS"trans_rigid_t2_to_t10GenericAffine.mat",1] \# {T1->T2}
else
	echo $TEMPLATE_LABELS_PD25_IN_DEEP7T" already exists. Skipping"
fi