amico_notebook.ipynb

{
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"source": [
"# I- DESCRIPTION"
]
},
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"source": [
"qMRinfo('amico'); % Describe the model"
]
},
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"source": [
"# II- MODEL PARAMETERS\n",
"## a- Create object"
]
},
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"source": [
"Model = amico;"
]
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"## Download sample data from OSF\n",
"> The current `Model` is an instance of `amico` class.\n",
" \n",
"You can manually download the sample data for `amico` [by clicking here](https:\/\/osf.io\/4s6rf\/download?version=4)."
]
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"dataDir = downloadData(Model,pwd);"
]
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"## b- Set protocol\n",
"> Protocol is set according to the example data\n",
" \n",
"%          |- amico object needs 1 protocol field(s) to be assigned:\n",
"%          |-   DiffusionData"
]
},
{
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"Gx = [0.0000; 0.0000; 0.6528; -0.3734; 0.6595; 0.4251; 0.9307; 0.2346; -0.5629; -0.1656; -0.9726; -0.0150; 0.1463; -0.2313; 0.7377; -0.7661; -0.1051; 0.0000; 0.3909; 0.1496; -0.9334; 0.1903; -0.7039; -0.5217; 0.9662; -0.3714; -0.7828; 0.8305; -0.3302; -0.2348; 0.0253; -0.5469; 0.7053; 0.0000; 0.3198; 0.7962; 0.8699; 0.6890; -0.9299; 0.0387; 0.3218; 0.3582; 0.8944; 0.4384; -0.3516; -0.1507; -0.5361; 0.5114; -0.0808; 0.0000; -0.0261; -0.4804; -0.8220; -0.3674; -0.8059; 0.9937; -0.9844; -0.4309; 0.1316; -0.0096; 0.6996; -0.6609; 0.8179; -0.7977; 0.4352; 0.0000; 0.3330; 0.5147; -0.8173; -0.5177; -0.0540; 0.0108; -0.0691; 0.8929; 0.6656; 0.3998; 0.2992; -0.6774; -0.3221; 0.5112; -0.1681; 0.0000; 0.8415; 0.2496; 0.6320; 0.1861; 0.4758; 0.7481; 0.9338; 0.6610; 0.6125; 0.6137; 0.6817; 0.0996; -0.9739; 0.8386; 0.2920; 0.0000; -0.7056; -0.2181; -0.6203; 0.0020; -0.1074; 0.2822; 0.4012; 0.5307; 0.5323; 0.9651; 0.0000];\n",
"% Gx is a vector of [109X1]\n",
"Gy = [0.0000; 0.0000; -0.6550; 0.1688; 0.7394; 0.0347; 0.0616; -0.8169; -0.0797; -0.8647; 0.0079; 0.9886; 0.7658; -0.5711; 0.5254; 0.5946; -0.9930; 0.0000; -0.4079; -0.3372; -0.2009; 0.7622; -0.4547; 0.4241; -0.2577; 0.9198; 0.6149; -0.2333; -0.8437; -0.5578; 0.1522; -0.7771; 0.6419; 0.0000; -0.6674; -0.0672; -0.1770; 0.4593; 0.3590; 0.4492; 0.4365; 0.2082; 0.4341; -0.8638; 0.8508; 0.5115; 0.3158; -0.7514; 0.9207; 0.0000; -0.9526; -0.8692; 0.3566; -0.3033; -0.5619; -0.0273; -0.1502; -0.9023; 0.1687; -0.1114; -0.7110; -0.2140; -0.3778; -0.1210; 0.6742; 0.0000; -0.5741; -0.6575; -0.5127; 0.4818; 0.5946; -0.8315; -0.7675; 0.2597; 0.3549; -0.8171; -0.0563; -0.1344; 0.2540; 0.6731; -0.9515; 0.0000; -0.4352; 0.9109; -0.0796; -0.9773; -0.8795; 0.6348; -0.2954; -0.0966; -0.4925; -0.1628; -0.4899; 0.3862; -0.2261; 0.5426; 0.9388; 0.0000; 0.1116; 0.9406; 0.7701; 0.3742; -0.4286; -0.6551; 0.7562; 0.4305; 0.4358; -0.2538; 0.0000];\n",
"% Gy is a vector of [109X1]\n",
"Gz = [0.0000; 0.0000; 0.3807; 0.9122; 0.1356; -0.9045; 0.3607; -0.5270; -0.8227; 0.4743; 0.2325; -0.1496; -0.6262; -0.7876; -0.4240; 0.2441; 0.0536; 0.0000; 0.8251; 0.9295; -0.2972; 0.6187; 0.5456; 0.7403; -0.0065; -0.1266; 0.0958; 0.5057; -0.4233; 0.7961; 0.9880; 0.3116; 0.3009; 0.0000; 0.6726; -0.6012; -0.4604; 0.5607; -0.0796; 0.8926; -0.8402; 0.9101; -0.1075; -0.2483; 0.3905; 0.8460; -0.7829; 0.4170; -0.3819; 0.0000; -0.3031; 0.1170; 0.4439; -0.8792; -0.1865; 0.1090; 0.0921; 0.0165; -0.9768; 0.9937; 0.0714; 0.7193; 0.4339; -0.5907; -0.5967; 0.0000; -0.7480; -0.5502; -0.2629; -0.7070; -0.8022; 0.5555; -0.6373; -0.3679; 0.6565; 0.4153; 0.9525; 0.7233; 0.9120; 0.5345; -0.2576; 0.0000; 0.3202; -0.3285; -0.7708; -0.1011; 0.0065; -0.1930; -0.2018; 0.7442; 0.6183; -0.7725; -0.5434; 0.9170; -0.0219; -0.0485; 0.1827; 0.0000; -0.6998; 0.2600; 0.1488; 0.9274; 0.8971; -0.7009; -0.5169; 0.7301; -0.7258; 0.0647; 0.0000];\n",
"% Gz is a vector of [109X1]\n",
"Gnorm = [0.0000; 0.0000; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0310; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0000; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0310; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0000; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0310; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0000; 0.0800; 0.0566; 0.0800; 0.0800; 0.0310; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0000; 0.0566; 0.0800; 0.0800; 0.0310; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0000; 0.0800; 0.0800; 0.0310; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0000; 0.0800; 0.0310; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0800; 0.0800; 0.0566; 0.0000];\n",
"% Gnorm is a vector of [109X1]\n",
"Delta = [0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308; 0.0308];\n",
"% Delta is a vector of [109X1]\n",
"delta = [0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128; 0.0128];\n",
"% delta is a vector of [109X1]\n",
"TE = [0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636; 0.0636];\n",
"% TE is a vector of [109X1]\n",
"Model.Prot.DiffusionData.Mat = [ Gx Gy Gz Gnorm Delta delta TE];\n",
"%%   "
]
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{
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"source": [
"# III- FIT EXPERIMENTAL DATASET\n",
"## a- Load experimental data\n",
"%          |- amico object needs 2 data input(s) to be assigned:\n",
"%          |-   DiffusionData\n",
"%          |-   Mask"
]
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"% DiffusionData.nii.gz contains [74   87   50  109] data.\n",
"data.DiffusionData=double(load_nii_data('amico_data\/DiffusionData.nii.gz'));\n",
"% Mask.nii.gz contains [74  87  50] data.\n",
"data.Mask=double(load_nii_data('amico_data\/Mask.nii.gz'));\n",
" "
]
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"## b- Fit experimental data\n",
"> This section will fit data."
]
},
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"source": [
"FitResults = FitData(data,Model,0);"
]
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"## c- Show fitting results\n",
"> * Output map will be displayed.\n",
" \n",
"> * If available, a graph will be displayed to show fitting in a voxel."
]
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"source": [
"qMRshowOutput(FitResults,data,Model);"
]
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"## d- Save results\n",
"> * qMR maps are saved in NIFTI and in a structure `FitResults.mat` that can be loaded in qMRLab graphical user interface.\n",
"> * Model object stores all the options and protocol\n",
"> * These objects can be easily shared or be used for simulation."
]
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"source": [
"FitResultsSave_nii(FitResults, 'amico_data\/DiffusionData.nii.gz');"
]
},
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"# IV- SIMULATIONS\n",
"> This section can be executed to run simulations for vfa_t1.\n",
" \n",
"## a- Single Voxel Curve\n",
"> Simulates single voxel curves:\n",
" \n",
"       1. Use equation to generate synthetic MRI data\n",
"       2. Add rician noise\n",
"       3. Fit and plot curve"
]
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"      x = struct;\n",
"      x.ficvf = 0.5;\n",
"      x.di = 1.7;\n",
"      x.kappa = 0.05;\n",
"      x.fiso = 0;\n",
"      x.diso = 3;\n",
"      x.b0 = 1;\n",
"      x.theta = 0.2;\n",
"      x.phi = 0;\n",
"       Opt.SNR = 50;\n",
"      % run simulation\n",
"      figure('Name','Single Voxel Curve Simulation');\n",
"      FitResult = Model.Sim_Single_Voxel_Curve(x,Opt);"
]
},
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"source": [
"## b- Sensitivity analysis\n",
"> Simulates sensitivity to fitted parameters: \n",
" \n",
"       1. Vary fitting parameters from lower (lb) to upper (ub) bound.\n",
"       2. Run Sim_Single_Voxel_Curve Nofruns times\n",
"       3. Compute mean and std across runs"
]
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"      %              ficvf         di            kappa         fiso          diso          b0            theta         phi           \n",
"      OptTable.st = [0.5           1.7           0.05          0             3             1             0.2           0]; % nominal values\n",
"      OptTable.fx = [0             1             1             1             1             1             1             1]; %vary ficvf...\n",
"      OptTable.lb = [0             1.3           0.05          0             1             0             0             0]; %...from 0\n",
"      OptTable.ub = [1             2.1           0.8           1             5             1e+03         3.1           3.1]; %...to 1\n",
"       Opt.SNR = 50;\n",
"       Opt.Nofrun = 5;\n",
"      % run simulation\n",
"      SimResults = Model.Sim_Sensitivity_Analysis(OptTable,Opt);\n",
"      figure('Name','Sensitivity Analysis');\n",
"      SimVaryPlot(SimResults, 'ficvf' ,'ficvf' );"
]
}
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