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joshuacwnewtonmguaypaq
joshuacwnewton
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mguaypaq
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Improve environment variable quoting by only quoting the variables themselves (#13)
Co-authored-by: Mathieu Guay-Paquet <mathieu.guaypaquet@gmail.com>
1 parent e92fb1e commit ede52e5

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Lines changed: 59 additions & 59 deletions

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‎multi_subject/process_data.sh‎

Lines changed: 53 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -45,21 +45,21 @@ label_if_does_not_exist() {
4545
# - If it doesn't, perform automatic labeling.
4646
# This allows you to add manual labels on a subject-by-subject basis without disrupting the pipeline.
4747
###
48-
local file="$1"
49-
local file_seg="$2"
48+
local file="${1}"
49+
local file_seg="${2}"
5050
# Update global variable with segmentation file name
51-
FILELABEL="${file}_labels"
52-
FILELABELMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${FILELABEL}-manual.nii.gz"
53-
echo "Looking for manual label: $FILELABELMANUAL"
54-
if [[ -e $FILELABELMANUAL ]]; then
51+
FILELABEL="${file}"_labels
52+
FILELABELMANUAL="${PATH_DATA}"/derivatives/labels/"${SUBJECT}"/anat/"${FILELABEL}"-manual.nii.gz
53+
echo "Looking for manual label: ${FILELABELMANUAL}"
54+
if [[ -e "${FILELABELMANUAL}" ]]; then
5555
echo "Found! Using manual labels."
56-
rsync -avzh $FILELABELMANUAL ${FILELABEL}.nii.gz
56+
rsync -avzh "${FILELABELMANUAL}" "${FILELABEL}".nii.gz
5757
else
5858
echo "Not found. Proceeding with automatic labeling."
5959
# Generate labeled segmentation
60-
sct_label_vertebrae -i ${file}.nii.gz -s ${file_seg}.nii.gz -c t2 -qc "${PATH_QC}" -qc-subject "${SUBJECT}"
60+
sct_label_vertebrae -i "${file}".nii.gz -s "${file_seg}".nii.gz -c t2 -qc "${PATH_QC}" -qc-subject "${SUBJECT}"
6161
# Create labels in the cord at C3 and C5 mid-vertebral levels
62-
sct_label_utils -i ${file_seg}_labeled.nii.gz -vert-body 3,5 -o ${FILELABEL}.nii.gz
62+
sct_label_utils -i "${file_seg}"_labeled.nii.gz -vert-body 3,5 -o "${FILELABEL}".nii.gz
6363
fi
6464
}
6565

@@ -70,21 +70,21 @@ segment_if_does_not_exist() {
7070
# - If it doesn't, perform automatic spinal cord segmentation.
7171
# This allows you to add manual segmentations on a subject-by-subject basis without disrupting the pipeline.
7272
###
73-
local file="$1"
74-
local contrast="$2"
73+
local file="${1}"
74+
local contrast="${2}"
7575
# Update global variable with segmentation file name
76-
FILESEG="${file}_seg"
77-
FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${FILESEG}-manual.nii.gz"
76+
FILESEG="${file}"_seg
77+
FILESEGMANUAL="${PATH_DATA}"/derivatives/labels/"${SUBJECT}"/anat/"${FILESEG}"-manual.nii.gz
7878
echo
79-
echo "Looking for manual segmentation: $FILESEGMANUAL"
80-
if [[ -e $FILESEGMANUAL ]]; then
79+
echo "Looking for manual segmentation: ${FILESEGMANUAL}"
80+
if [[ -e "${FILESEGMANUAL}" ]]; then
8181
echo "Found! Using manual segmentation."
82-
rsync -avzh $FILESEGMANUAL ${FILESEG}.nii.gz
83-
sct_qc -i ${file}.nii.gz -s ${FILESEG}.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
82+
rsync -avzh "${FILESEGMANUAL}" "${FILESEG}".nii.gz
83+
sct_qc -i "${file}".nii.gz -s "${FILESEG}".nii.gz -p sct_deepseg_sc -qc "${PATH_QC}" -qc-subject "${SUBJECT}"
8484
else
8585
echo "Not found. Proceeding with automatic segmentation."
8686
# Segment spinal cord
87-
sct_deepseg_sc -i ${file}.nii.gz -c $contrast -qc ${PATH_QC} -qc-subject ${SUBJECT}
87+
sct_deepseg_sc -i "${file}".nii.gz -c "${contrast}" -qc "${PATH_QC}" -qc-subject "${SUBJECT}"
8888
fi
8989
}
9090

@@ -93,61 +93,61 @@ segment_if_does_not_exist() {
9393
# ======================================================================================================================
9494

9595
# Retrieve input params
96-
SUBJECT=$1
96+
SUBJECT="${1}"
9797

9898
# get starting time:
99-
start=`date +%s`
99+
start="$(date +%s)"
100100

101101
# Display useful info for the log, such as SCT version, RAM and CPU cores available
102102
sct_check_dependencies -short
103103

104104
# Go to folder where data will be copied and processed
105-
cd $PATH_DATA_PROCESSED
105+
cd "${PATH_DATA_PROCESSED}"
106106
# Copy source images
107-
rsync -avzh $PATH_DATA/$SUBJECT .
107+
rsync -avzh "${PATH_DATA}"/"${SUBJECT}" .
108108

109109

110110
# T2w
111111
# ======================================================================================================================
112-
cd "${SUBJECT}/anat/"
113-
file_t2="${SUBJECT}_T2w"
112+
cd "${SUBJECT}"/anat/
113+
file_t2="${SUBJECT}"_T2w
114114
# Segment spinal cord (only if it does not exist)
115115
segment_if_does_not_exist "${file_t2}" "t2"
116116
file_t2_seg="${FILESEG}"
117117
# Create labels in the cord at C2 and C5 mid-vertebral levels (only if it does not exist)
118118
label_if_does_not_exist "${file_t2}" "${file_t2_seg}"
119119
file_label="${FILELABEL}"
120120
# Register to template
121-
sct_register_to_template -i "${file_t2}.nii.gz" -s "${file_t2_seg}.nii.gz" -l "${file_label}.nii.gz" -c t2 \
121+
sct_register_to_template -i "${file_t2}".nii.gz -s "${file_t2_seg}".nii.gz -l "${file_label}".nii.gz -c t2 \
122122
-param step=1,type=seg,algo=centermassrot:step=2,type=im,algo=syn,iter=5,slicewise=1,metric=CC,smooth=0 \
123123
-qc "${PATH_QC}"
124124
# Warp template
125125
# Note: we don't need the white matter atlas at this point, therefore use flag "-a 0"
126-
sct_warp_template -d "${file_t2}.nii.gz" -w warp_template2anat.nii.gz -a 0 -ofolder label_T2w -qc "${PATH_QC}"
126+
sct_warp_template -d "${file_t2}".nii.gz -w warp_template2anat.nii.gz -a 0 -ofolder label_T2w -qc "${PATH_QC}"
127127
# Compute average CSA between C2 and C3 levels (append across subjects)
128-
sct_process_segmentation -i "${file_t2_seg}.nii.gz" -vert 2:3 -vertfile label_T2w/template/PAM50_levels.nii.gz \
129-
-o "${PATH_RESULTS}/CSA.csv" -append 1 -qc "${PATH_QC}"
128+
sct_process_segmentation -i "${file_t2_seg}".nii.gz -vert 2:3 -vertfile label_T2w/template/PAM50_levels.nii.gz \
129+
-o "${PATH_RESULTS}"/CSA.csv -append 1 -qc "${PATH_QC}"
130130

131131
# MT
132132
# ======================================================================================================================
133-
file_mt1="${SUBJECT}_acq-MTon_MTS"
134-
file_mt0="${SUBJECT}_acq-MToff_MTS"
133+
file_mt1="${SUBJECT}"_acq-MTon_MTS
134+
file_mt0="${SUBJECT}"_acq-MToff_MTS
135135
# Segment spinal cord
136136
segment_if_does_not_exist "${file_mt1}" "t2s"
137-
file_mt1_seg=$FILESEG
137+
file_mt1_seg="${FILESEG}"
138138
# Create mask
139-
sct_create_mask -i "${file_mt1}.nii.gz" -p centerline,"${file_mt1_seg}.nii.gz" -size 45mm
139+
sct_create_mask -i "${file_mt1}".nii.gz -p centerline,"${file_mt1_seg}".nii.gz -size 45mm
140140
# Crop data for faster processing
141-
sct_crop_image -i "${file_mt1}.nii.gz" -m "mask_${file_mt1}.nii.gz" -o "${file_mt1}_crop.nii.gz"
142-
sct_crop_image -i "${file_mt1_seg}.nii.gz" -m "mask_${file_mt1}.nii.gz" -o "${file_mt1}_crop_seg.nii.gz"
143-
file_mt1="${file_mt1}_crop"
141+
sct_crop_image -i "${file_mt1}".nii.gz -m "mask_${file_mt1}".nii.gz -o "${file_mt1}"_crop.nii.gz
142+
sct_crop_image -i "${file_mt1_seg}".nii.gz -m "mask_${file_mt1}".nii.gz -o "${file_mt1}"_crop_seg.nii.gz
143+
file_mt1="${file_mt1}"_crop
144144
# Register mt0->mt1
145145
# Tips: here we only use rigid transformation because both images have very
146146
# similar sequence parameters. We don't want to use SyN/BSplineSyN to avoid
147147
# introducing spurious deformations.
148-
sct_register_multimodal -i "${file_mt0}.nii.gz" \
149-
-d "${file_mt1}.nii.gz" \
150-
-dseg "${file_mt1}_seg.nii.gz" \
148+
sct_register_multimodal -i "${file_mt0}".nii.gz \
149+
-d "${file_mt1}".nii.gz \
150+
-dseg "${file_mt1}"_seg.nii.gz \
151151
-param step=1,type=im,algo=rigid,slicewise=1,metric=CC \
152152
-x spline \
153153
-qc "${PATH_QC}"
@@ -156,30 +156,30 @@ sct_register_multimodal -i "${file_mt0}.nii.gz" \
156156
# Tips: First step: slicereg based on images, with large smoothing to capture
157157
# potential motion between anat and mt, then at second step: bpslinesyn in order to
158158
# adapt the shape of the cord to the mt modality (in case there are distortions between anat and mt).
159-
sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz" \
160-
-iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" \
161-
-d "${file_mt1}.nii.gz" \
162-
-dseg "${file_mt1}_seg.nii.gz" \
159+
sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2.nii.gz \
160+
-iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz \
161+
-d "${file_mt1}".nii.gz \
162+
-dseg "${file_mt1}"_seg.nii.gz \
163163
-param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 \
164164
-initwarp warp_template2anat.nii.gz \
165165
-initwarpinv warp_anat2template.nii.gz \
166166
-qc "${PATH_QC}"
167167
# Rename warping fields for clarity
168-
mv "warp_PAM50_t22${file_mt1}.nii.gz" warp_template2mt.nii.gz
169-
mv "warp_${file_mt1}2PAM50_t2.nii.gz" warp_mt2template.nii.gz
168+
mv warp_PAM50_t22"${file_mt1}".nii.gz warp_template2mt.nii.gz
169+
mv warp_"${file_mt1}"2PAM50_t2.nii.gz warp_mt2template.nii.gz
170170
# Warp template
171-
sct_warp_template -d "${file_mt1}.nii.gz" -w warp_template2mt.nii.gz -ofolder label_MT -qc "${PATH_QC}"
171+
sct_warp_template -d "${file_mt1}".nii.gz -w warp_template2mt.nii.gz -ofolder label_MT -qc "${PATH_QC}"
172172
# Compute mtr
173-
sct_compute_mtr -mt0 "${file_mt0}_reg.nii.gz" -mt1 "${file_mt1}.nii.gz"
173+
sct_compute_mtr -mt0 "${file_mt0}"_reg.nii.gz -mt1 "${file_mt1}".nii.gz
174174
# compute MTR in dorsal columns between levels C2 and C5 (append across subjects)
175175
sct_extract_metric -i mtr.nii.gz -f label_MT/atlas -l 53 -vert 2:5 -vertfile label_MT/template/PAM50_levels.nii.gz \
176176
-method map -o "${PATH_RESULTS}/MTR_in_DC.csv" -append 1
177177

178178
# Verify presence of output files and write log file if error
179179
# ======================================================================================================================
180180
FILES_TO_CHECK=(
181-
"$file_t2_seg.nii.gz"
182-
"mtr.nii.gz"
181+
"${file_t2_seg}".nii.gz
182+
mtr.nii.gz
183183
)
184184
for file in "${FILES_TO_CHECK[@]}"; do
185185
if [ ! -e "${file}" ]; then
@@ -188,11 +188,11 @@ for file in "${FILES_TO_CHECK[@]}"; do
188188
done
189189

190190
# Display useful info for the log
191-
end=`date +%s`
192-
runtime=$((end-start))
191+
end="$(date +%s)"
192+
runtime="$((end-start))"
193193
echo
194194
echo "~~~"
195-
echo "SCT version: `sct_version`"
196-
echo "Ran on: `uname -nsr`"
197-
echo "Duration: $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
195+
echo "SCT version: $(sct_version)"
196+
echo "Ran on: $(uname -nsr)"
197+
echo "Duration: $((runtime / 3600))hrs $(( (runtime / 60) % 60))min $((runtime % 60))sec"
198198
echo "~~~"

‎single_subject/batch_single_subject.sh‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@ echo -e "\nStarted at: $(date +%x_%r)"
2323
# Source: https://unix.stackexchange.com/a/497540
2424
if ! command -v fsleyes > /dev/null; then
2525
fsleyes() {
26-
printf 'WARNING: FSLeyes is not installed, so the following command was skipped:\nfsleyes %s\n' "$*";
26+
printf 'WARNING: FSLeyes is not installed, so the following command was skipped:\nfsleyes %s\n' "${*@Q}";
2727
};
2828
fi
2929

@@ -136,7 +136,7 @@ sct_create_mask -i mt1.nii.gz -p centerline,mt1_seg.nii.gz -size 35mm -f cylinde
136136

137137
# Register template->mt1. The flag -initwarp ../t2/warp_template2anat.nii.gz initializes the registration using the
138138
# template->t2 transformation which was previously estimated
139-
sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
139+
sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -m mask_mt1.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
140140
# Tips: Here we only use the segmentations (type=seg) to minimize the sensitivity of the registration procedure to
141141
# image artifacts.
142142
# Tips: Step 1: algo=centermass to align source and destination segmentations, then Step 2: algo=bpslinesyn to adapt the
@@ -228,13 +228,13 @@ sct_extract_metric -i t2s.nii.gz -f t2s_gmseg.nii.gz -method bin -z 2:12 -o t2s_
228228

229229
# Register template->t2s (using warping field generated from template<->t2 registration)
230230
# Tips: Here we use the WM seg for the iseg/dseg fields in order to account for both the cord and the GM shape.
231-
sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2s.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_wm.nii.gz" -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz -param step=1,type=seg,algo=rigid:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc ~/qc_singleSubj
231+
sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2s.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_wm.nii.gz -d t2s.nii.gz -dseg t2s_wmseg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2t2s.nii.gz -owarpinv warp_t2s2template.nii.gz -param step=1,type=seg,algo=rigid:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc ~/qc_singleSubj
232232
# Warp template
233233
sct_warp_template -d t2s.nii.gz -w warp_template2t2s.nii.gz -qc ~/qc_singleSubj
234234

235235
cd ../mt
236236
# Register template->mt via t2s to account for GM segmentation
237-
sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
237+
sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii.gz -dseg mt1_seg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -owarp warp_template2mt.nii.gz -qc ~/qc_singleSubj
238238
# Warp template
239239
sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -qc ~/qc_singleSubj
240240
# Check results
@@ -279,7 +279,7 @@ sct_deepseg_sc -i dmri_moco_dwi_mean.nii.gz -c dwi -qc ~/qc_singleSubj
279279
# -param, so it will not make a difference here)
280280
# Note: the flag “-initwarpinv" provides a transformation dmri->template, in case you would like to bring all your DTI
281281
# metrics in the PAM50 space (e.g. group averaging of FA maps)
282-
sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t1.nii.gz" -iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" -d dmri_moco_dwi_mean.nii.gz -dseg dmri_moco_dwi_mean_seg.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -initwarpinv ../t2s/warp_t2s2template.nii.gz -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc ~/qc_singleSubj
282+
sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t1.nii.gz -iseg "${SCT_DIR}"/data/PAM50/template/PAM50_cord.nii.gz -d dmri_moco_dwi_mean.nii.gz -dseg dmri_moco_dwi_mean_seg.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -initwarpinv ../t2s/warp_t2s2template.nii.gz -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc ~/qc_singleSubj
283283
# Warp template (so 'label/atlas' can be used to extract metrics)
284284
sct_warp_template -d dmri_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc ~/qc_singleSubj
285285
# Check results in the QC report
@@ -313,7 +313,7 @@ sct_fmri_moco -i fmri.nii.gz -m mask_fmri.nii.gz -qc ~/qc_singleSubj -qc-seg t2_
313313
# ANTs_SyN superpower to find a suitable transformation between the PAM50_t2s and the fMRI scan. We don't want to
314314
# put too many iterations because this registration is very sensitive to the artifacts (drop out) in the image.
315315
# Also, we want a 3D transformation (not 2D) because we need the through-z regularization.
316-
sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t2s.nii.gz" -d fmri_moco_mean.nii.gz -dseg t2_seg_reg.nii.gz -param step=1,type=im,algo=syn,metric=CC,iter=5,slicewise=0 -initwarp ../t2s/warp_template2t2s.nii.gz -initwarpinv ../t2s/warp_t2s2template.nii.gz -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz -qc ~/qc_singleSubj
316+
sct_register_multimodal -i "${SCT_DIR}"/data/PAM50/template/PAM50_t2s.nii.gz -d fmri_moco_mean.nii.gz -dseg t2_seg_reg.nii.gz -param step=1,type=im,algo=syn,metric=CC,iter=5,slicewise=0 -initwarp ../t2s/warp_template2t2s.nii.gz -initwarpinv ../t2s/warp_t2s2template.nii.gz -owarp warp_template2fmri.nii.gz -owarpinv warp_fmri2template.nii.gz -qc ~/qc_singleSubj
317317
# Check results in the QC report
318318

319319
# Warp template with the spinal levels (-s 1)

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