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"source": [
"# I- DESCRIPTION"
]
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"source": [
"qMRinfo('mt_sat'); % Describe the model"
]
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"# II- MODEL PARAMETERS\n",
"## a- Create object"
]
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"Model = mt_sat;"
]
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"source": [
"## Download sample data from OSF\n",
"> The current `Model` is an instance of `mt_sat` class.\n",
" \n",
"You can manually download the sample data for `mt_sat` [by clicking here](https:\/\/osf.io\/c5wdb\/download?version=3)."
]
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"source": [
"dataDir = downloadData(Model,pwd);"
]
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"## b- Set protocol\n",
"> Protocol is set according to the example data\n",
" \n",
"%          |- mt_sat object needs 3 protocol field(s) to be assigned:\n",
"%          |-   MTw\n",
"%          |-   T1w\n",
"%          |-   PDw"
]
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"FlipAngle = 6;\n",
"TR  = 0.028;\n",
"Model.Prot.MTw.Mat = [ FlipAngle TR ];\n",
"%%   \n",
"FlipAngle = 20;\n",
"TR = 0.018;\n",
"Model.Prot.T1w.Mat = [ FlipAngle TR];\n",
"%%   \n",
"FlipAngle = 6;\n",
"TR = 0.028;\n",
"Model.Prot.PDw.Mat = [ FlipAngle TR];\n",
"%%   "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# III- FIT EXPERIMENTAL DATASET\n",
"## a- Load experimental data\n",
"%          |- mt_sat object needs 5 data input(s) to be assigned:\n",
"%          |-   MTw\n",
"%          |-   T1w\n",
"%          |-   PDw\n",
"%          |-   B1map\n",
"%          |-   Mask"
]
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"% MTw.nii.gz contains [128  128   96] data.\n",
"data.MTw=double(load_nii_data('mt_sat_data\/MTw.nii.gz'));\n",
"% T1w.nii.gz contains [128  128   96] data.\n",
"data.T1w=double(load_nii_data('mt_sat_data\/T1w.nii.gz'));\n",
"% PDw.nii.gz contains [128  128   96] data.\n",
"data.PDw=double(load_nii_data('mt_sat_data\/PDw.nii.gz'));\n",
" "
]
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"cell_type": "markdown",
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"source": [
"## b- Fit experimental data\n",
"> This section will fit data."
]
},
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"cell_type": "code",
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"source": [
"FitResults = FitData(data,Model,0);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 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."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
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"outputs": [],
"source": [
"qMRshowOutput(FitResults,data,Model);"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## 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."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
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"outputs": [],
"source": [
"FitResultsSave_nii(FitResults, 'mt_sat_data\/MTw.nii.gz');"
]
}
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