mp2rage_notebook.ipynb

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"# I- DESCRIPTION"
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"qMRinfo('mp2rage'); % Describe the model"
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"# II- MODEL PARAMETERS\n",
"## a- Create object"
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"Model = mp2rage;"
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"## Download sample data from OSF\n",
"> The current `Model` is an instance of `mp2rage` class.\n",
" \n",
"You can manually download the sample data for `mp2rage` [by clicking here](https:\/\/osf.io\/k3shf\/download?version=1)."
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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",
"%          |- mp2rage object needs 5 protocol field(s) to be assigned:\n",
"%          |-   Hardware\n",
"%          |-   RepetitionTimes\n",
"%          |-   Timing\n",
"%          |-   Sequence\n",
"%          |-   NumberOfShots"
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"B0  = 7;\n",
"Model.Prot.Hardware.Mat = [ B0 ];\n",
"%%   \n",
"Inv  = 6;\n",
"Exc  = 0.0067;\n",
"Model.Prot.RepetitionTimes.Mat = [ Inv  Exc ];\n",
"%%   \n",
"InversionTimes  = [0.8000; 2.7000];\n",
"% InversionTimes (s) is a vector of [2X1]\n",
"Model.Prot.Timing.Mat = [ InversionTimes ];\n",
"%%   \n",
"FlipAngles = [4.0000; 5.0000];\n",
"% FlipAngles is a vector of [2X1]\n",
"Model.Prot.Sequence.Mat = [ FlipAngles];\n",
"%%   \n",
"Pre = 35;\n",
"Post = 72;\n",
"Model.Prot.NumberOfShots.Mat = [ Pre Post];\n",
"%%   "
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"# III- FIT EXPERIMENTAL DATASET\n",
"## a- Load experimental data\n",
"%          |- mp2rage object needs 7 data input(s) to be assigned:\n",
"%          |-   MP2RAGE\n",
"%          |-   INV1mag\n",
"%          |-   INV1phase\n",
"%          |-   INV2mag\n",
"%          |-   INV2phase\n",
"%          |-   B1map\n",
"%          |-   Mask"
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" \n",
"% MP2RAGE.mat contains [143  218    2] data.\n",
" load('mp2rage_data\/MP2RAGE.mat');\n",
"% B1map.mat contains [143  218    2] data.\n",
" load('mp2rage_data\/B1map.mat');\n",
" data.MP2RAGE= double(MP2RAGE);\n",
" data.B1map= double(B1map);"
]
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"## b- Fit experimental data\n",
"> This section will fit data."
]
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"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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"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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"FitResultsSave_nii(FitResults);"
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