-
Notifications
You must be signed in to change notification settings - Fork 0
/
dwi-03-anat2dwi.sh
403 lines (340 loc) · 17.3 KB
/
dwi-03-anat2dwi.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
#!/bin/bash
#SBATCH --job-name=anat2dwi
#SBATCH --mem=8G
#SBATCH --partition=luna-cpu-short
#SBATCH --qos=anw-cpu
#SBATCH --cpus-per-task=8
#SBATCH --time=00-01:00:00
#SBATCH --nice=2000
#SBATCH --output=anat2dwi_%A.log
###############################################################################
# source software #
###############################################################################
module load fsl/6.0.6.5
module load FreeSurfer/7.3.2-centos8_x86_64
module load ANTs/2.4.1
module load art
module load Anaconda3/2022.05
conda activate /scratch/anw/share/python-env/mrtrix
# Define color variables
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[0;33m'
BLUE='\033[34m'
NC='\033[0m' # No Color
# Initialize variables
bidsdir=""
outputdir=""
workdir=""
freesurferdir=""
subj=""
scriptdir=""
# input variables
# Parse command line arguments
while getopts ":i:o:f:w:s:c:" opt; do
case $opt in
i)
bidsdir="$OPTARG"
;;
o)
outputdir="$OPTARG"
;;
f)
freesurferdir="$OPTARG"
;;
w)
workdir="$OPTARG"
;;
s)
subj="$OPTARG"
;;
c)
scriptdir="$OPTARG"
;;
\?)
echo "Invalid option -$OPTARG" >&2
;;
esac
done
#scriptdir=/data/anw/anw-gold/NP/projects/data_chris/Tmult/scripts
synthstrippath=/scratch/anw/share-np/fmridenoiser/synthstrip.1.2.sif
atlasdir=/data/anw/anw-gold/NP/doorgeefluik/atlas4FreeSurfer
threads=8
###############################################################################
##############################
# warp atlases to FreeSurfer
##############################
echo -e "${BLUE}transfer FreeSurfer output to work directory${NC}"
mkdir -p ${workdir}/${subj}
if [[ ! -d ${freesurferdir}/${subj}/mri ]]; then
echo -e "${RED}FreeSurfer output not available${NC}"
echo -e "${RED}processing stopped for ${subj}${NC}"
sleep 1
exit
fi
rsync -az --ignore-existing ${freesurferdir}/${subj} ${workdir}/${subj}/freesurfer/
export SUBJECTS_DIR=${workdir}/${subj}/freesurfer
mkdir -p ${SUBJECTS_DIR}/${subj}/dwi
echo
echo -e "${BLUE}Warp atlases to FreeSurfer output${NC}"
sbatch --wait ${scriptdir}/atlas2FreeSurfer.sh ${SUBJECTS_DIR} ${subj}
echo
echo -e "${BLUE}continue with anat to dwi registration${NC}"
echo
for dwidir in ${bidsdir}/${subj}/{,ses*/}dwi; do
if [ ! -d ${dwidir} ]; then
continue
fi
sessiondir=$(dirname ${dwidir})
echo
echo ${sessiondir}
echo
session=$(echo "${sessiondir}" | grep -oP "(?<=${subj}/).*")
if [ -z ${session} ]; then
sessionpath=/
sessionfile=_
else
sessionpath=/${session}/
sessionfile=_${session}_
fi
# check if output already available #
if (( $( ls ${outputdir}/dwi-preproc/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-*_dseg.nii.gz 2>/dev/null | wc -l ) > 0 )); then
echo -e "${GREEN}${subj}${sessionfile} already has atlasses in dwi-space${NC}"
echo -e "...skip...${NC}"
echo
continue
fi
##---------------------------------##
mkdir -p "${workdir}/${subj}${sessionpath}dwi"
mkdir -p "${workdir}/${subj}${sessionpath}anat"
mkdir -p "${workdir}/${subj}${sessionpath}figures"
mkdir -p "${workdir}/${subj}/anat"
mkdir -p "${workdir}/${subj}/figures"
mkdir -p "${outputdir}/dwi-preproc/${subj}/logs"
cd ${workdir}/${subj}${sessionpath}
# assumes that there is only ONE!! FreeSurfer output per subject
if [ ! -f ${outputdir}/dwi-preproc/${subj}/anat/${subj}_desc-5tt-hsvs_probseg.nii.gz ] ||
[ ! -f ${outputdir}/dwi-preproc/${subj}/anat/${subj}_desc-gmwm_probseg.nii.gz ] ||
[ ! -f ${outputdir}/dwi-preproc/${subj}/anat/${subj}_desc-wm_probseg.nii.gz ]; then
# using T1 from Freesurfer directory
if [ ! -f ${workdir}/${subj}/anat/${subj}_desc-preproc_T1w.nii.gz ] ||
[ ! -f ${workdir}/${subj}/anat/${subj}_desc-brain_T1w.nii.gz ]; then
rsync -azv --ignore-existing \
${freesurferdir}/${subj}/mri/T1.mgz \
${freesurferdir}/${subj}/mri/brain.mgz \
${workdir}/${subj}/anat
cd ${workdir}/${subj}/anat
# convert to nii.gz
mri_convert --in_type mgz --out_type nii \
--out_orientation RAS brain.mgz ${subj}_desc-brain_T1w.nii.gz
mri_convert --in_type mgz --out_type nii \
--out_orientation RAS T1.mgz ${subj}_desc-preproc_T1w.nii.gz
# binarize
fslmaths ${subj}_desc-brain_T1w.nii.gz -bin ${subj}_desc-brain_mask.nii.gz
rm T1.mgz brain.mgz
# check overay
slicer ${subj}_desc-brain_T1w.nii.gz ${subj}_desc-brain_T1w.nii.gz \
-a ${workdir}/${subj}/figures/${subj}_BETQC.png
fi
if [ ! -f ${workdir}/${subj}/anat/${subj}_desc-5tt-hsvs_probseg.nii.gz ]; then
# review settings
echo -e "${YELLOW}Prepare 5TT estimation${NC}"
5ttgen hsvs ${workdir}/${subj}/freesurfer/${subj} \
${subj}_5TThsvs.nii.gz \
-hippocampi aseg -thalami aseg -white_stem -nthreads ${threads} \
-nocrop -nocleanup -scratch ${workdir}/${subj}/temp_5ttgen -force
rm ${subj}_5TThsvs.nii.gz
${scriptdir}/modify_5ttgen.sh ${workdir}/${subj}/temp_5ttgen ${workdir}/${subj}/freesurfer/ ${subj}
mv ${workdir}/${subj}/temp_5ttgen/${subj}_5TThsvs.nii.gz ${workdir}/${subj}/anat/${subj}_desc-5tt-hsvs_probseg.nii.gz
rm -r ${workdir}/${subj}/temp_5ttgen
fi
cd ${workdir}/${subj}/anat
if [ ! -f ${workdir}/${subj}/anat/${subj}_desc-gmwm_probseg.nii.gz ]; then
5tt2gmwmi ${subj}_desc-5tt-hsvs_probseg.nii.gz ${subj}_desc-gmwm_probseg.nii.gz \
-nthreads ${threads} -info -force
fi
# reorient to FSL RAS
fslreorient2std ${subj}_desc-5tt-hsvs_probseg.nii.gz ${subj}_desc-5tt-hsvs_probseg.nii.gz
fslreorient2std ${subj}_desc-gmwm_probseg.nii.gz ${subj}_desc-gmwm_probseg.nii.gz
# used in BBR to speed up and prevent NaN errors
fslroi ${subj}_desc-5tt-hsvs_probseg.nii.gz \
${subj}_desc-wm_probseg.nii.gz 2 1
# transfer from work directory to output directory
rsync -a *.nii.gz ${outputdir}/dwi-preproc/${subj}/anat
fi
###########################
# T1 to DWI registration
###########################
rsync -a ${outputdir}/dwi-preproc/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc* \
${workdir}/${subj}${sessionpath}dwi
rsync -a --ignore-existing ${outputdir}/dwi-preproc/${subj}/anat/* ${workdir}/${subj}/anat
if [ -d ${outputdir}/dwi-preproc/${subj}${sessionpath}xfms ]; then
rsync -a ${outputdir}/dwi-preproc/${subj}${sessionpath}xfms ${workdir}/${subj}${sessionpath}
fi
cd ${workdir}/${subj}${sessionpath}dwi
# create mean b0 (nodif)
if [ ! -f ${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz ] ||
[ ! -f ${subj}${sessionfile}space-dwi_desc-brain_mask.nii.gz ]; then
dwiextract -nthreads ${threads} \
${subj}${sessionfile}space-dwi_desc-preproc_dwi.nii.gz - -bzero \
-fslgrad ${subj}${sessionfile}space-dwi_desc-preproc_dwi.bvec \
${subj}${sessionfile}space-dwi_desc-preproc_dwi.bval | mrmath - mean ${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz -axis 3
# skullstrip mean b0 (nodif_brain)
apptainer run --cleanenv ${synthstrippath} \
-i ${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
-o ${subj}${sessionfile}space-dwi_desc-nodif-brain_dwi.nii.gz \
--mask ${subj}${sessionfile}space-dwi_desc-brain_mask.nii.gz
fi
mkdir -p ${workdir}/${subj}${sessionpath}xfms
if [ ! -f ${workdir}/${subj}${sessionpath}xfms/${subj}${sessionfile}epireg.mat ] ||
[ ! -f ${workdir}/${subj}${sessionpath}xfms/${subj}${sessionfile}epireg_inversed.mat ]; then
echo -e "${BLUE}anat to DWI registration${NC}"
# ants better?
flirt -in ${workdir}/${subj}/anat/${subj}_desc-brain_T1w.nii.gz \
-ref ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
-omat ${workdir}/${subj}${sessionpath}xfms/T1w-2-diff.mat \
-searchrx -90 90 -searchry -90 90 -searchrz -90 90 \
-dof 6 -cost corratio
convert_xfm -omat ${workdir}/${subj}${sessionpath}xfms/diff-2-T1w.mat \
-inverse ${workdir}/${subj}${sessionpath}xfms/T1w-2-diff.mat
epi_reg --epi=${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
--t1=${workdir}/${subj}/anat/${subj}_desc-preproc_T1w.nii.gz \
--t1brain=${workdir}/${subj}/anat/${subj}_desc-brain_T1w.nii.gz \
--wmseg=${workdir}/${subj}/anat/${subj}_desc-wm_probseg.nii.gz \
--out=${workdir}/${subj}${sessionpath}xfms/${subj}${sessionfile}epireg
convert_xfm -omat ${workdir}/${subj}${sessionpath}xfms/${subj}${sessionfile}epireg_inversed.mat \
-inverse ${workdir}/${subj}${sessionpath}xfms/${subj}${sessionfile}epireg.mat
fi
if [ ! -f ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-5tt-hsvs_probseg.nii.gz ] ||
[ ! -f ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-gmwm_probseg.nii.gz ]; then
for label in 5tt-hsvs gmwm; do
echo -e "${BLUE}warp ${label} to DWI-space${NC}"
flirt -in ${workdir}/${subj}/anat/${subj}_desc-${label}_probseg.nii.gz \
-ref ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz -applyxfm \
-init ${workdir}/${subj}${sessionpath}xfms/${subj}${sessionfile}epireg_inversed.mat \
-out ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-${label}_probseg.nii.gz -interp nearestneighbour
#mrconvert ${workdir}/${subj}${sessionpath}/dwi/${subj}_space-dwi_desc-${label}_probseg.nii.gz \
#${workdir}/${subj}${sessionpath}/dwi/${subj}_space-dwi_desc-${label}_probseg.mif
done
fi
# QA
if [ ! -f ${outputdir}/dwi-preproc/${subj}${sessionpath}figures/${subj}${sessionfile}5tt-overlay.png ]; then
5tt2vis ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-5tt-hsvs_probseg.nii.gz \
${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}5ttvis.mif
mrview ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}5ttvis.mif \
-capture.prefix ${subj}_5tt- \
-noannot -mode 2 -capture.grab -exit
mv ${subj}_5tt-*.png ${outputdir}/dwi-preproc/${subj}${sessionpath}figures/${subj}${sessionfile}5tt-overlay.png
rm ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}5ttvis.mif
fi
# mask fit
if [ ! -f ${outputdir}/dwi-preproc/${subj}${sessionpath}figures/${subj}${sessionfile}maskQC.png ]; then
slicer ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif-brain_dwi.nii.gz \
${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-brain_mask.nii.gz \
-A 2000 ${outputdir}/dwi-preproc/${subj}${sessionpath}figures/${subj}${sessionfile}maskQC.png
fi
# transfer to output directory
mkdir -p ${outputdir}/dwi-preproc/${subj}/anat
mkdir -p ${outputdir}/dwi-preproc/${subj}${sessionpath}dwi/
rsync -a ${workdir}/${subj}/anat/* ${outputdir}/dwi-preproc/${subj}/anat
rsync -a ${workdir}/${subj}${sessionpath}xfms ${outputdir}/dwi-preproc/${subj}${sessionpath}
# gmwm hsvs do not exist?
rsync -a ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-gmwm_probseg.nii.gz \
${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-5tt-hsvs_probseg.nii.gz \
${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-brain_mask.nii.gz \
${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif-brain_dwi.nii.gz \
${outputdir}/dwi-preproc/${subj}${sessionpath}dwi/
##################################
# FREESURFER to DWI registration
##################################
if [ ! -f ${SUBJECTS_DIR}/${subj}/dwi/${subj}${sessionfile}register.dat ]; then
bbregister --s ${subj} \
--mov ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
--init-best --reg ${SUBJECTS_DIR}/${subj}/dwi/${subj}${sessionfile}register.dat --dti
fi
# warp atlases to dwi space
for atlas in BNA 300P7N 300P17N 400P7N 400P17N aparc500; do
if [ ! -f ${SUBJECTS_DIR}/${subj}/mri/${atlas}+aseg.mgz ]; then
echo
echo -e "${YELLOW}WARNING! atlas: ${atlas} - not available in FreeSurfer directory of ${subj}${NC}"
continue
else
if [ ! -f ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_dseg.nii.gz ]; then
# register atlas to DWI
mri_vol2vol --mov ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
--targ ${SUBJECTS_DIR}/${subj}/mri/${atlas}+aseg.mgz \
--o ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_temp.nii.gz \
--reg ${SUBJECTS_DIR}/${subj}/dwi/${subj}${sessionfile}register.dat --inv --no-save-reg --interp nearest
if [[ ${atlas} == "300P7N" ]]; then
ID="Schaefer_300P7N"
elif [[ ${atlas} == "300P17N" ]]; then
ID="Schaefer_300P17N"
elif [[ ${atlas} == "400P7N" ]]; then
ID="Schaefer_400P7N"
elif [[ ${atlas} == "400P17N" ]]; then
ID="Schaefer_400P17N"
elif [[ ${atlas} == "200P7N" ]]; then
ID="Schaefer_200P7N"
elif [[ ${atlas} == "100P7N" ]]; then
ID="Schaefer_100P7N"
elif [[ ${atlas} == "aparc500" ]]; then
ID="aparc500_labels"
elif [[ ${atlas} == "BNA" ]]; then
ID="BNA_labels"
elif [[ ${atlas} == "BNA+cerebellum" ]]; then
ID="BNA+CER_labels"
else
echo "atlas not found!"
exit
fi
if [[ ${ID} != *"Schaefer"* ]]; then
# convert and sort labels
labelconvert ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_temp.nii.gz \
${atlasdir}/${atlas}/${ID}_orig.txt \
${atlasdir}/${atlas}/${ID}_modified.txt \
${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_dseg.nii.gz -force
else
labelconvert ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_temp.nii.gz \
${atlasdir}/Schaefer/${ID}_orig.txt \
${atlasdir}/Schaefer/${ID}_modified.txt \
${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_dseg.nii.gz -force
fi
rm ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_temp.nii.gz
fi
fi
# QC registration of atlas to dwi
${scriptdir}/check_atlasreg.py \
--subjid ${subj}${sessionfile} \
--atlas ${atlas} \
--atlas_image ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_dseg.nii.gz \
--nodif ${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
--output ${outputdir}/dwi-preproc/${subj}${sessionpath}figures
fslstats -K ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_dseg.nii.gz \
${workdir}/${subj}${sessionpath}dwi/${subj}${sessionfile}space-dwi_desc-nodif_dwi.nii.gz \
-V >roivols.txt
# delete line with Unknown and print columns 1 and 2
if [[ ${ID} != *"Schaefer"* ]]; then
labelfile=${atlasdir}/${atlas}/${ID}_modified.txt
else
labelfile=${atlasdir}/Schaefer/${ID}_modified.txt
fi
grep -v "Unknown" ${labelfile} | awk '{ print $1,$2 }' >labels.txt
paste labels.txt roivols.txt >${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas-${atlas}_roivols.txt
rm roivols.txt labels.txt
# NEED TO CHECK THIS!
# echo "check roi volumes ${atlas}"
# ${scriptdir}/check_roivols_luna.py -subjid ${subj} -atlas ${atlas} \
# -file ${workdir}/QC/${subjbase}_${atlas}_roivols.txt
done
# transfer files
rsync -av ${workdir}/${subj}${sessionpath}anat/${subj}${sessionfile}space-dwi_atlas* \
${outputdir}/dwi-preproc/${subj}${sessionpath}anat/
rsync -av --ignore-existing ${SUBJECTS_DIR}/${subj} ${freesurferdir}
done
# clean up
chmod -R u+w ${workdir}/${subj}/freesurfer/fsaverage
rm -rf ${workdir}/${subj}
echo "-----------------------------------"
echo "finished anat2dwi subject = ${subj}"
echo "-----------------------------------"