Commit 75398e99153639b384c541cac8dcbb0fbd7ebe52 - bart

update to grasp script (courtesy of tobias block) Martin Uecker 8 years ago

1 changed file(s) with 27 addition(s) and 30 deletion(s). Raw diff Collapse all Expand all

+27

-30

scripts/grasp.sh less more

18	18	export ITER=30
19	19	export REG=0.05
20	20	SCALE=0.6
21		LOGFILE=/dev/null
	21	LOGFILE=/dev/stdout
22	22	MAXPROC=4
23	23	MAXTHREADS=4
24	24

100	100	exit 1
101	101	fi
102	102
103		if [ ! -e $TOOLBOX_PATH/fft ] ; then
	103	if [ ! -e $TOOLBOX_PATH/bart ] ; then
104	104	echo "\$TOOLBOX_PATH is not set correctly!" >&2
105	105	exit 1
106	106	fi

116	116	{
117	117
118	118	# read TWIX file
119		twixread -A $input grasp
	119	bart twixread -A $input grasp
120	120
121	121	export READ=$(tail -n1 grasp.hdr \| cut -f1 -d" ")
122	122	export COILS=$(tail -n1 grasp.hdr \| cut -f4 -d" ")

132	132	#rm grasp.* grasp2.*
133	133
134	134	# inverse FFT along 3rd dimension
135		fft -i -u $(bitmask 2) grasp grasp_hybrid
	135	bart fft -i -u $(bart bitmask 2) grasp grasp_hybrid
136	136	rm grasp.cfl grasp.hdr
137	137
138	138	SLICES=$(tail -n1 grasp_hybrid.hdr \| cut -f3 -d" ")
139	139
140	140
141	141	# create trajectory with 400 spokes and 2x oversampling
142		traj -G -x$READ -y$CALIB r
143		scale $SCALE r rcalib
	142	bart traj -G -x$READ -y$CALIB r
	143	bart scale $SCALE r rcalib
144	144
145	145	# create trajectory with 2064 spokes and 2x oversampling
146		traj -G -x$READ -y$(($SPOKES * $PHASES)) r
147		scale $SCALE r r2
	146	bart traj -G -x$READ -y$(($SPOKES * $PHASES)) r
	147	bart scale $SCALE r r2
148	148
149	149	# split off time dimension into index 10
150		reshape $(bitmask 2 10) $SPOKES $PHASES r2 rfull
	150	bart reshape $(bart bitmask 2 10) $SPOKES $PHASES r2 rfull
151	151
152	152	# number of threads per slice
153	153	export OMP_NUM_THREADS=$MAXTHREADS

155	155	calib_slice()
156	156	{
157	157	# extract slice
158		slice 2 $1 grasp_hybrid grasp1-$1
	158	bart slice 2 $1 grasp_hybrid grasp1-$1
159	159
160	160	# extract first $CALIB spokes
161		extract 1 $(($SKIP + 0)) $(($SKIP + $CALIB - 1)) grasp1-$1 grasp2-$1
	161	bart extract 1 $(($SKIP + 0)) $(($SKIP + $CALIB - 1)) grasp1-$1 grasp2-$1
162	162
163	163	# reshape dimensions
164		reshape $(bitmask 0 1 2 3) 1 $READ $CALIB $COILS grasp2-$1 grasp3-$1
	164	bart reshape $(bart bitmask 0 1 2 3) 1 $READ $CALIB $COILS grasp2-$1 grasp3-$1
165	165
166	166	# apply inverse nufft to first $CALIB spokes
167		nufft -i -t rcalib grasp3-$1 img-$1.coo
	167	bart nufft -i -t rcalib grasp3-$1 img-$1.coo
168	168	}
169	169
170	170	recon_slice()
171	171	{
172	172	# extract sensitivities for slice
173		slice 2 $1 sens sens-$1
	173	bart slice 2 $1 sens sens-$1
174	174
175	175	# extract spokes and split-off time dim
176		extract 1 $(($SKIP + 0)) $(($SKIP + $SPOKES * $PHASES - 1)) grasp1-$1 grasp2-$1
177		reshape $(bitmask 1 2) $SPOKES $PHASES grasp2-$1 grasp1-$1
	176	bart extract 1 $(($SKIP + 0)) $(($SKIP + $SPOKES * $PHASES - 1)) grasp1-$1 grasp2-$1
	177	bart reshape $(bart bitmask 1 2) $SPOKES $PHASES grasp2-$1 grasp1-$1
178	178
179	179	# move time dimensions to dim 10 and reshape
180		transpose 2 10 grasp1-$1 grasp2-$1
181		reshape $(bitmask 0 1 2) 1 $READ $SPOKES grasp2-$1 grasp1-$1
	180	bart transpose 2 10 grasp1-$1 grasp2-$1
	181	bart reshape $(bart bitmask 0 1 2) 1 $READ $SPOKES grasp2-$1 grasp1-$1
182	182	rm grasp2-$1.cfl grasp2-$1.hdr
183	183
184	184	# reconstruction with tv penality along dimension 10
185	185	# old (v0.2.08):
186	186	# pics -S -d5 -lv -u10. -r$REG -R$(bitmask 10) -i$ITER -t rfull grasp1-$1 sens-$1 i-$1.coo
187	187	# new (v0.2.09):
188		pics -S -d5 -u10. -RT:$(bitmask 10):0:$REG -i$ITER -t rfull grasp1-$1 sens-$1 i-$1.coo
	188	bart pics -S -d5 -u10. -RT:$(bart bitmask 10):0:$REG -i$ITER -t rfull grasp1-$1 sens-$1 i-$1.coo
189	189
190	190	# clean up temp files
191	191	rm -$1.cfl -$1.hdr

198	198	seq -w 0 $(($SLICES - 1)) \| xargs -I {} -P $MAXPROC bash -c "calib_slice {}"
199	199
200	200	# transform back to k-space and compute sensitivities
201		join 2 img-*.coo img
202		fft -u $(bitmask 0 1 2) img ksp
	201	bart join 2 img-*.coo img
	202	bart fft -u $(bart bitmask 0 1 2) img ksp
203	203
204	204	#ecalib -S -c0.8 -m1 -r20 ksp sens
205	205
206	206	# transpose because we already support off-center calibration region
207	207	# in dim 0 but here we might have it in 2
208		transpose 0 2 ksp ksp2
209		ecalib -S -c0.8 -m1 -r20 ksp2 sens2
210		transpose 0 2 sens2 sens
	208	bart transpose 0 2 ksp ksp2
	209	bart ecalib -S -c0.8 -m1 -r20 ksp2 sens2
	210	bart transpose 0 2 sens2 sens
211	211
212	212	# loop over slices
213	213	seq -w 0 $(($SLICES - 1)) \| xargs -I {} -P $MAXPROC bash -c "recon_slice {}"
214	214	#echo 20 \| xargs -i --max-procs=$MAXPROC bash -c "recon_slice {}"
215	215
216	216	# join slices back together
217		join 2 i-*.coo $output
	217	bart join 2 i-*.coo $output
218	218
219	219	# generate dicoms
220	220	#for s in $(seq -w 0 $(($SLICES - 1))) ; do
221	221	# for p in $(seq -w 0 $(($PHASES - 1))) ; do
222		#
223		# slice 10 $p i-$s.coo i-$p-$s.coo
224		# toimg i-$p-$s.coo $output-$p$-$s.dcm
	222	# bart slice 10 $p i-$s.coo i-$p-$s.coo
	223	# bart toimg i-$p-$s.coo $output.series$p.slice$s.dcm
225	224	# done
226	225	#done
227	226
228	227	} > $LOGFILE
229	228
230	229	exit 0
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