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change scaling and command line for T2 moba to be consistent with mob…
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…afit
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@uecker
uecker committed Sep 20, 2024
1 parent d3dd873 commit 0759d7e
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Showing 4 changed files with 26 additions and 22 deletions.
16 changes: 12 additions & 4 deletions src/moba.c
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Original file line number Diff line number Diff line change
Expand Up @@ -195,21 +195,23 @@ int main_moba(int argc, char* argv[argc])

opt_reg_init(&ropts);

bool t2_old_flag = false;

const struct opt_s opts[] = {

//FIXME: Sort options into optimization and others interface
{ 'r', NULL, true, OPT_SPECIAL, opt_reg_moba, &ropts, "<T>:A:B:C", "generalized regularization options (-rh for help)" },
OPT_SELECT('L', enum mdb_t, &conf.mode, MDB_T1, "T1 mapping using model-based look-locker"),
OPT_SELECT('P', enum mdb_t, &conf.mode, MDB_T1_PHY, "T1 mapping using reparameterized (M0, R1, alpha) model-based look-locker (TR required!)"),
OPT_SELECT('F', enum mdb_t, &conf.mode, MDB_T2, "T2 mapping using model-based Fast Spin Echo"),
OPT_SET('F', &t2_old_flag, "(T2 mapping using model-based Fast Spin Echo)"),
OPT_SELECT('T', enum mdb_t, &conf.mode, MDB_T2, "T2 mapping using model-based Fast Spin Echo"),
OPT_SELECT('G', enum mdb_t, &conf.mode, MDB_MGRE, "T2* mapping using model-based multiple gradient echo"),
OPT_SELECT('D', enum mdb_t, &conf.mode, MDB_IR_MGRE, "Joint T1 and T2* mapping using model-based IR multiple gradient echo"),
OPTL_SELECT(0, "bloch", enum mdb_t, &conf.mode, MDB_BLOCH, "Bloch model-based reconstruction"),
OPT_UINT('m', &conf.mgre_model, "model", "Select the MGRE model from enum { WF = 0, WFR2S, WF2R2S, R2S, PHASEDIFF, ..., WF_fB0, WF_R2S, T1_R2S, W_T1_F_T1_RS2 } [default: WFR2S]"),
OPT_PINT('l', &conf.opt_reg, "\b1/-l2", " toggle l1-wavelet or l2 regularization."), // extra spaces needed because of backsapce \b earlier
OPT_PINT('i', &conf.iter, "iter", "Number of Newton steps"),
OPTL_FLOAT('R', "reduction", &conf.redu, "redu", "reduction factor"),
OPT_FLOAT('T', &conf.damping, "damp", "damping on temporal frames"),
OPT_FLOAT('j', &conf.alpha_min, "minreg", "Minimum regularization parameter"),
OPT_FLOAT('u', &conf.rho, "rho", "ADMM rho [default: 0.01]"),
OPT_PINT('C', &conf.inner_iter, "iter", "inner iterations"),
Expand All @@ -230,6 +232,7 @@ int main_moba(int argc, char* argv[argc])
OPTL_PINT(0, "pusteps", &conf.pusteps, "ud", "Number of partial update steps for IRGNM"),
OPTL_FLOAT(0, "ratio", &conf.ratio, "f:[0;1]", "Ratio of partial updates: ratio*<updated-map> + (1-ratio)*<previous-map>"),
OPTL_FLOAT(0, "l1val", &conf.l1val, "f", "Regularization scaling of l1 wavelet (default: 1.)"),
OPTL_FLOAT(0, "temporal_damping", &conf.damping, "f", "Temporal damping factor."),
OPTL_INT(0, "multi-gpu", &(conf.num_gpu), "num", "(number of gpus to use)"),
OPT_INFILE('I', &init_file, "init", "File for initialization"),
OPT_INFILE('t', &traj_file, "traj", "K-space trajectory"),
Expand Down Expand Up @@ -269,6 +272,8 @@ int main_moba(int argc, char* argv[argc])
if (use_compat_to_version("v0.6.00"))
conf.scaling_M0 = 2.;

if (t2_old_flag)
conf.mode = MDB_T2;

if (conf.ropts->r > 0)
conf.algo = ALGO_ADMM;
Expand All @@ -287,7 +292,10 @@ int main_moba(int argc, char* argv[argc])
complex float* kspace_data = load_cfl(ksp_file, DIMS, ksp_dims);

long TI_dims[DIMS];
const complex float* TI = load_cfl(TI_file, DIMS, TI_dims);
complex float* TI = load_cfl(TI_file, DIMS, TI_dims);

if (t2_old_flag)
md_zsmul(DIMS, TI_dims, TI, TI, 10.);

assert(TI_dims[TE_DIM] == ksp_dims[TE_DIM]);
assert(1 == ksp_dims[MAPS_DIM]);
Expand Down Expand Up @@ -405,7 +413,7 @@ int main_moba(int argc, char* argv[argc])
md_clear(DIMS, coil_dims, sens, CFL_SIZE);
}

md_zfill(DIMS, img_dims, img, 1.0);
md_zfill(DIMS, img_dims, img, 1.);

complex float* k_grid_data = anon_cfl("", DIMS, grid_dims);

Expand Down
20 changes: 8 additions & 12 deletions src/moba/T2fun.c
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Original file line number Diff line number Diff line change
Expand Up @@ -49,13 +49,11 @@ struct T2_s {
complex float* dz;

struct multiplace_array_s* TE;

float scaling_z;
};

DEF_TYPEID(T2_s);

// Calculate Model: rho .*exp(-scaling_z.*z.*TE)
// Calculate Model: rho .*exp(-z.*TE)
static void T2_fun(const nlop_data_t* _data, complex float* dst, const complex float* src)
{
struct T2_s* data = CAST_DOWN(T2_s, _data);
Expand Down Expand Up @@ -83,11 +81,11 @@ static void T2_fun(const nlop_data_t* _data, complex float* dst, const complex f

complex float* tmp_map = md_alloc_sameplace(data->N, data->map_dims, CFL_SIZE, dst);

// -1*scaling_z.*z
md_zsmul(data->N, data->map_dims, tmp_map, data->z, -1. * data->scaling_z);
// -1*z
md_zsmul(data->N, data->map_dims, tmp_map, data->z, -1.);

complex float* tmp_exp = md_alloc_sameplace(data->N, data->out_dims, CFL_SIZE, dst);
// exp(-TE.*scaling_z.*z)
// exp(-TE.*z)
md_zmul2(data->N, data->out_dims, data->out_strs, tmp_exp, data->map_strs, tmp_map, data->TE_strs, multiplace_read(data->TE, dst));

md_free(tmp_map);
Expand All @@ -99,13 +97,13 @@ static void T2_fun(const nlop_data_t* _data, complex float* dst, const complex f
md_zsmul(data->N, data->out_dims, data->drho, tmp_exp, 1.0);

// model:
// rho.*exp(-TE.*scaling_z.*z)
// rho.*exp(-TE.*z)
md_zmul2(data->N, data->out_dims, data->out_strs, dst, data->map_strs, data->rho, data->out_strs, tmp_exp);

// dz: z' = -rho.*scaling_z.*TE.*exp(-TE.*scaling_z.*z)
// TE.*exp(-TE.*scaling_z.*z),
// dz: z' = -rho.*TE.*exp(-TE.*z)
// TE.*exp(-TE.*z),
md_zmul2(data->N, data->out_dims, data->out_strs, tmp_exp, data->out_strs, tmp_exp, data->TE_strs, multiplace_read(data->TE, dst));
md_zsmul(data->N, data->out_dims, tmp_exp, tmp_exp, -1. * data->scaling_z);
md_zsmul(data->N, data->out_dims, tmp_exp, tmp_exp, -1.);
md_zmul2(data->N, data->out_dims, data->out_strs, data->dz, data->map_strs, data->rho, data->out_strs, tmp_exp);

md_free(tmp_exp);
Expand Down Expand Up @@ -241,7 +239,5 @@ struct nlop_s* nlop_T2_create(int N, const long map_dims[N], const long out_dims
data->dz = NULL;
data->TE = multiplace_move(N, TE_dims, CFL_SIZE, TE);

data->scaling_z = 10.;

return nlop_create(N, out_dims, N, in_dims, CAST_UP(PTR_PASS(data)), T2_fun, T2_der, T2_adj, NULL, NULL, T2_del);
}
2 changes: 1 addition & 1 deletion src/moba/recon.c
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,7 @@ static struct mobamod exp_create(const long dims[DIMS], const complex float* mas

complex float* TE2 = md_alloc(DIMS, edims, CFL_SIZE);

md_zsmul(DIMS, edims, TE2, TE, -10.);
md_zsmul(DIMS, edims, TE2, TE, -1.);


// chain T2 model
Expand Down
10 changes: 5 additions & 5 deletions tests/moba.mk
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Original file line number Diff line number Diff line change
Expand Up @@ -167,13 +167,13 @@ tests/test-moba-t2: phantom signal fmac fft ones index scale moba slice invert n
$(TOOLDIR)/ones 6 16 16 1 1 1 16 psf.ra ;\
$(TOOLDIR)/index 5 16 tmp1.ra ;\
$(TOOLDIR)/scale 0.01 tmp1.ra TE.ra ;\
$(TOOLDIR)/moba -F -i10 -f1 -C30 --scale_data=5000. --scale_psf=1000. --normalize_scaling -d4 -p psf.ra k_space.ra TE.ra reco.ra ;\
$(TOOLDIR)/moba -T -i10 -f1 -C50 --scale_data=5000. --scale_psf=1000. --normalize_scaling -d4 -p psf.ra k_space.ra TE.ra reco.ra ;\
$(TOOLDIR)/slice 6 1 reco.ra R2.ra ;\
$(TOOLDIR)/invert R2.ra T2.ra ;\
$(TOOLDIR)/phantom -x16 -c circ.ra ;\
$(TOOLDIR)/fmac T2.ra circ.ra masked.ra ;\
$(TOOLDIR)/scale -- 0.9 circ.ra ref.ra ;\
$(TOOLDIR)/nrmse -t 0.0008 masked.ra ref.ra ;\
$(TOOLDIR)/scale -- 0.09 circ.ra ref.ra ;\
$(TOOLDIR)/nrmse -t 0.002 ref.ra masked.ra ;\
rm *.ra ; cd .. ; rmdir $(TESTS_TMP)
touch $@

Expand All @@ -189,7 +189,7 @@ tests/test-moba-meco-noncart-r2s: traj scale phantom signal fmac index extract m
$(TOOLDIR)/index 5 8 tmp1.ra ;\
$(TOOLDIR)/scale 1.6 tmp1.ra tmp2.ra ;\
$(TOOLDIR)/extract 5 1 8 tmp2.ra TE.ra ;\
$(TOOLDIR)/moba -G -m3 -rQ:1 -rS:0 -rW:3:64:1 -i10 -C100 -u0.0001 -R3 -T 0.9 -o1.5 -k --kfilter-2 -t traj.ra data.ra TE.ra reco.ra ;\
$(TOOLDIR)/moba -G -m3 -rQ:1 -rS:0 -rW:3:64:1 -i10 -C100 -u0.0001 -R3 --temporal_damping 0.9 -o1.5 -k --kfilter-2 -t traj.ra data.ra TE.ra reco.ra ;\
$(TOOLDIR)/slice 6 1 reco.ra R2S.ra ;\
$(TOOLDIR)/resize -c 0 8 1 8 R2S.ra R2S_crop.ra ;\
$(TOOLDIR)/phantom -x8 -c circ.ra ;\
Expand All @@ -211,7 +211,7 @@ tests/test-moba-meco-noncart-wfr2s: traj scale phantom signal fmac index extract
$(TOOLDIR)/index 5 8 tmp1.ra ;\
$(TOOLDIR)/scale 1.6 tmp1.ra tmp2.ra ;\
$(TOOLDIR)/extract 5 1 8 tmp2.ra TE.ra ;\
$(TOOLDIR)/moba -G -m1 -rQ:1 -rS:0 -rW:3:64:1 -i10 -C100 -u0.0001 -R3 -T0.9 -o1.5 -k --kfilter-2 -t traj.ra data.ra TE.ra reco.ra ;\
$(TOOLDIR)/moba -G -m1 -rQ:1 -rS:0 -rW:3:64:1 -i10 -C100 -u0.0001 -R3 --temporal_damping 0.9 -o1.5 -k --kfilter-2 -t traj.ra data.ra TE.ra reco.ra ;\
$(TOOLDIR)/resize -c 0 8 1 8 reco.ra reco_crop.ra ;\
$(TOOLDIR)/slice 6 0 reco_crop.ra W.ra ;\
$(TOOLDIR)/slice 6 1 reco_crop.ra F.ra ;\
Expand Down

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