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deface.bash
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#!/bin/bash
START_TIME=`date`
#BIDS_DIR_FACE=/autofs/vast/gerenuk/pwighton/fsm-bids/20221006-heudiconv
#BIDS_DIR_DEFACE=/autofs/vast/gerenuk/pwighton/fsm-bids/20221031-deface-wip
#DERIVATIVES_DIR=/autofs/vast/gerenuk/pwighton/fsm-bids/20221031-deface-wip/derivatives/mideface
#WORK_DIR=/autofs/vast/gerenuk/pwighton/fsm-bids/20221031-deface-wip/work
# Both $BIDS_DIR_FACE and $WORK_DIR contain sensitive information that should not
# be shared.
# - $BIDS_DIR_FACE contains the original defaced images in BIDS format
# - $WORK_DIR contains before/after pngs to QA the defacing process
BIDS_DIR_FACE=/home/paul/lcn/20221104-fsm-bids-face
WORK_DIR=/home/paul/lcn/20221105-fsm-bids-deface/work
# Both these dirs should not contain sensitive information
BIDS_DIR_DEFACE=/home/paul/lcn/20221105-fsm-bids-deface/bids
DERIVATIVES_DIR=${BIDS_DIR_DEFACE}/derivatives/mideface
# Use the obfuscated subject list
SUBJECT_LIST=/home/paul/lcn/git/fsm2bids/subjects-obfuscated.txt
ORIG_DIR=`pwd`
mkdir -p $BIDS_DIR_DEFACE
mkdir -p $DERIVATIVES_DIR
mkdir -p $WORK_DIR
SUB=$1
#for SUB in `cat ${SUBJECT_LIST}`
#do
echo "Working on subject: " $SUB
mkdir -p $DERIVATIVES_DIR/$SUB/anat
mkdir -p $BIDS_DIR_DEFACE/$SUB/anat
cd $DERIVATIVES_DIR/$SUB/anat
##### Deface gre3d #####
## Deface the first GRE echo, save the work dir and generate QA pics
if test -f "$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE.nii.gz"; then
mkdir -p $WORK_DIR/$SUB/acq-gre3d_echo-1_part-mag
cd $WORK_DIR/$SUB/acq-gre3d_echo-1_part-mag
mideface \
--i $BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE.nii.gz \
--odir $WORK_DIR/$SUB/acq-gre3d_echo-1_part-mag \
--pics \
--code ${SUB}
## Copy/convert face mask and defaced echo 1 image to the right spot
mri_convert \
$WORK_DIR/$SUB/acq-gre3d_echo-1_part-mag/face.mask.mgz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE_facemask.nii.gz
mri_convert \
$WORK_DIR/$SUB/acq-gre3d_echo-1_part-mag/defaced.mgz \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE.nii.gz
## Apply the facemask to deface the t2star map
mideface \
--apply \
$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-gre3d_T2starmap.nii.gz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE_facemask.nii.gz \
regheader \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-gre3d_T2starmap.nii.gz
## Apply the facemask to deface mag echos 2-12
for ECHO in 2 3 4 5 6 7 8 9 10 11 12
do
mideface \
--apply \
$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-gre3d_echo-${ECHO}_part-mag_MEGRE.nii.gz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE_facemask.nii.gz \
regheader \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-gre3d_echo-${ECHO}_part-mag_MEGRE.nii.gz \
--nii.gz
done
## Create an 'mul-facemask', that can be multipled with orig phase images to deaface
fscalc \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE_facemask.nii.gz \
not \
--o $WORK_DIR/$SUB/acq-gre3d_echo-1_part-mag/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE_facemask-mul.nii.gz
## Apply the mul-facemask to deface all phase echos
for ECHO in 1 2 3 4 5 6 7 8 9 10 11 12
do
# deface with multiply operator
fscalc $BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-gre3d_echo-${ECHO}_part-phase_MEGRE.nii.gz \
mul $WORK_DIR/$SUB/acq-gre3d_echo-1_part-mag/${SUB}_acq-gre3d_echo-1_part-mag_MEGRE_facemask-mul.nii.gz \
--o $BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-gre3d_echo-${ECHO}_part-phase_MEGRE.nii.gz
done
fi
##### Deface mp2rage #####
## Deface the second inversion, save the work dir and generate QA pics
if test -f "$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-mp2rage_inv-2_MP2RAGE.nii.gz"; then
mkdir -p $WORK_DIR/$SUB/acq-mp2rage_inv-2
cd $WORK_DIR/$SUB/acq-mp2rage_inv-2
mideface \
--i $BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-mp2rage_inv-2_MP2RAGE.nii.gz \
--odir $WORK_DIR/$SUB/acq-mp2rage_inv-2 \
--pics \
--code ${SUB}
## Copy/convert face mask and defaced second inversion image to the right spot
mri_convert \
$WORK_DIR/$SUB/acq-mp2rage_inv-2/face.mask.mgz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-mp2rage_inv-2_MP2RAGE_facemask.nii.gz
mri_convert \
$WORK_DIR/$SUB/acq-mp2rage_inv-2/defaced.mgz \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-mp2rage_inv-2_MP2RAGE.nii.gz
## Apply the facemask to the other mp2rage contrasts
for MP2CONTRAST in inv-1_MP2RAGE T1map UNIT1
do
mideface \
--apply \
$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-mp2rage_${MP2CONTRAST}.nii.gz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-mp2rage_inv-2_MP2RAGE_facemask.nii.gz \
regheader \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-mp2rage_${MP2CONTRAST}.nii.gz \
--nii.gz
done
fi
##### Deface vNav mprage #####
## Deface the RMS image, save the work dir and generate QA pics
if test -f "$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-mprageVnav_T1wRMS.nii.gz"; then
mkdir -p $WORK_DIR/$SUB/acq-mprageVnav_T1wRMS
cd $WORK_DIR/$SUB/acq-mprageVnav_T1wRMS
mideface \
--i $BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-mprageVnav_T1wRMS.nii.gz \
--odir $WORK_DIR/$SUB/acq-mprageVnav_T1wRMS \
--pics \
--code ${SUB}
## Copy/convert face mask and defaced echo 1 image to the right spot
mri_convert \
$WORK_DIR/$SUB/acq-mprageVnav_T1wRMS/face.mask.mgz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-mprageVnav_T1wRMS_facemask.nii.gz
mri_convert \
$WORK_DIR/$SUB/acq-mprageVnav_T1wRMS/defaced.mgz \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-mprageVnav_T1wRMS.nii.gz
## Apply the facemask to the other vNav MPRAGE contrasts
for T1WCONTRAST in echo-1_part-mag echo-2_part-mag echo-3_part-mag echo-4_part-mag
do
mideface \
--apply \
$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-mprageVnav_${T1WCONTRAST}_T1w.nii.gz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-mprageVnav_T1wRMS_facemask.nii.gz \
regheader \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-mprageVnav_${T1WCONTRAST}_T1w.nii.gz \
--nii.gz
done
## Create an 'mul-facemask', that can be multipled with orig phase images to deaface
fscalc \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-mprageVnav_T1wRMS_facemask.nii.gz \
not \
--o $WORK_DIR/$SUB/acq-mprageVnav_T1wRMS/${SUB}_acq-mprageVnav_T1wRMS_facemask-mul.nii.gz
## Apply the mul-facemask to deface all phase echos
for T1WCONTRAST in echo-1_part-phase echo-2_part-phase echo-3_part-phase echo-4_part-phase
do
# Deface with mul op
fscalc $BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-mprageVnav_${T1WCONTRAST}_T1w.nii.gz \
mul $WORK_DIR/$SUB/acq-mprageVnav_T1wRMS/${SUB}_acq-mprageVnav_T1wRMS_facemask-mul.nii.gz \
--o $BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-mprageVnav_${T1WCONTRAST}_T1w.nii.gz
done
fi
##### Deface t2 flair #####
if test -f "$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-t2flair_T2w.nii.gz"; then
mkdir -p $WORK_DIR/$SUB/acq-t2flair
cd $WORK_DIR/$SUB/acq-t2flair
mideface \
--i $BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-t2flair_T2w.nii.gz \
--odir $WORK_DIR/$SUB/acq-t2flair \
--pics \
--code ${SUB}
## Copy/convert face mask and defaced echo 1 image to the right spot
mri_convert \
$WORK_DIR/$SUB/acq-t2flair/face.mask.mgz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-t2flair_T2w_facemask.nii.gz
mri_convert \
$WORK_DIR/$SUB/acq-t2flair/defaced.mgz \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-t2flair_T2w.nii.gz
fi
##### Deface vNav t2 space #####
if test -f "$BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-t2spaceVnav_T2w.nii.gz"; then
mkdir -p $WORK_DIR/$SUB/acq-t2spaceVnav
cd $WORK_DIR/$SUB/acq-t2spaceVnav
mideface \
--i $BIDS_DIR_FACE/$SUB/anat/${SUB}_acq-t2spaceVnav_T2w.nii.gz \
--odir $WORK_DIR/$SUB/acq-t2spaceVnav \
--pics \
--code ${SUB}
## Copy/convert face mask and defaced echo 1 image to the right spot
mri_convert \
$WORK_DIR/$SUB/acq-t2spaceVnav/face.mask.mgz \
$DERIVATIVES_DIR/$SUB/anat/${SUB}_acq-t2spaceVnav_T2w_facemask.nii.gz
mri_convert \
$WORK_DIR/$SUB/acq-t2spaceVnav/defaced.mgz \
$BIDS_DIR_DEFACE/$SUB/anat/${SUB}_acq-t2spaceVnav_T2w.nii.gz
fi
## Copy over the jsons to go with the defaced nifits we just made
cp $BIDS_DIR_FACE/$SUB/anat/*.json $BIDS_DIR_DEFACE/$SUB/anat/
## Copy over the dirs we are not defacing
cp -R $BIDS_DIR_FACE/$SUB/dwi $BIDS_DIR_DEFACE/$SUB/dwi
cp -R $BIDS_DIR_FACE/$SUB/fmap $BIDS_DIR_DEFACE/$SUB/fmap
cp -R $BIDS_DIR_FACE/$SUB/func $BIDS_DIR_DEFACE/$SUB/func
## Copy over top-level files
cp $BIDS_DIR_FACE/$SUB/${SUB}* $BIDS_DIR_DEFACE/$SUB/
#end of "for SUB in `cat ${SUBJECT_LIST}`"
#done
cd $ORIG_DIR
END_TIME=`date`
echo Start Time: $START_TIME
echo End Time: $END_TIME