diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox index 7c16b548b7..24752bc1ce 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/Manual.dox @@ -1,35 +1,53 @@ /** \page org_mitk_views_pharmacokinetics_concentration_mri The DCE Concentration Curve Converter View \imageMacro{pharmacokinetics_concentration_doc.svg,"Icon of the DCE Concentration Curve Converter View",3.0} \tableofcontents \section org_mitk_views_pharmacokinetics_concentration_mri_overview Overview This view offers a dedicated tool for the conversion of DCE MR image signal intensities to contrast agent (CA) concentration. -It contains a subset of the conversion tools for T1-weighted signal intensities, which are a part of the DCE MR Perfusion Datafit View (see \ref FIT_DCE_Settings_concentration). +It contains a subset of the conversion tools for T1-weighted signal intensities, which are also a part of the DCE MR Perfusion Datafit View see \ref org_mitk_views_pharmacokinetics_mri ). Additionally, it allows for the conversion between T2-weighted MR signal intensities and contrast agent concentration. \section org_mitk_views_pharmacokinetics_concentration_mri_Contact Contact information If you have any questions, need support, find a bug or have a feature request, feel free to contact us at www.mitk.org. \section org_mitk_views_pharmacokinetics_concentration_mri_T1_conversion Conversion of T1-weighted MRI data -\imageMacro{concentration_curve_converter_T1_weighted4D.png,"Example screenshot of the conversion of T1-weighted MR images",3.0} +\imageMacro{concentration_curve_converter_T1_weighted4D.png,"Example screenshot of the conversion of T1-weighted MR images",3.0 } The view offers the choice between a <i>3D Image</i> and a <i>4D image</i>. If a 4D image is selected, the <i>Selected Time Series</i> needs to be specified. -In this case, the baseline image is automatically extracted as the first time point image of the time series. +For all 4D images the range of the time points which are part of the baseline can be specified. The baseline signal <i>S<sub>BL</sub></i> will be averaged between the signal of the time points within this range. +If not specified, the baseline signal <i>S<sub>BL</sub></i> is set as the signal of the first time point image of the time series. In case of a 3D image to be converted, additionally to the selected 3D image a <i>Baseline Image (without CA)</i> has to be specified.\n\n -In the configuration section, the following types of conversion can be chosen: -- <i>Absolute Signal Enhancement</i>: The contrast agent concentration <i>c</i> is calculated according to the formula: <i>c = k*(S(t)-S(0))</i>, where <i>S(t)</i> is the dynamic T1-weighted signal intensity, <i>S(0)</i> the baseline signal and <i>k</i> a user-defined conversion factor. -- <i>Relative Signal Enhancement</i>: The contrast agent concentration <i>c</i> is calculated according to the formula: <i>c = k*(S(t)-S(0))/S(0)</i>, where <i>S(t)</i> is the dynamic T1-weighted signal intensity, <i>S(0)</i> the baseline signal and <i>k</i> a user-defined conversion factor. -- <i>Turbo FLASH Sequence</i>: The conversion from signal <i>S(t)</i> to contrast agent concentration <i>c</i> is calculated according to the turboFLASH (ultrafast gradient echo) sequence specific formula. +The following types of conversion can be chosen: +- <i>Absolute Signal Enhancement</i>: The dynamic contrast agent concentration <i>C(t)</i> is calculated according to the formula: <i>C(t) = k*(S(t)-S<sub>BL</sub>)</i>, where <i>S(t)</i> is the dynamic T1-weighted signal intensity, <i>S<sub>BL</sub></i> the baseline signal and <i>k</i> a user-defined conversion factor. +- <i>Relative Signal Enhancement</i>: The dynamic contrast agent concentration <i>C(t)</i> is calculated according to the formula: <i>C(t) = k*(S(t)-S<sub>BL</sub>)/S<sub>BL</sub></i>, where <i>S(t)</i> is the dynamic T1-weighted signal intensity, <i>S<sub>BL</sub></i> the baseline signal and <i>k</i> a user-defined conversion factor. +- <i>Variable Flip Angle</i>: This conversion uses the method described in \ref org_mitk_views_pharmacokinetics_concentration_mri_lit_ref1 "[1]". As additional input to the dynamic time series, +a proton density weighted (PDW) image is provided, which has been acquired pre-contrast with the same sequence parameters as for the +dynamic image but a smaller flip angle. Both flip angles are provided by the user. +Furthermore, the repetition time <i>TR</i> and the longitudinal relaxivity <i> r<sub>1</sub></i> are required as input.<br> +It is assumed that the MR data has been acquired according to the spoiled gradient recalled echo model. +The sequence formulas for the PDW image signal and for the baseline signal of the dynamic time series are two equations with two unknowns: +the pre-contrast R<sub>1</sub>-relaxation rate <i>R<sub>10</sub></i> and the signal scaling factor <i>S<sub>0</sub></i>. These are calculated by solving the system of equations.<br> +With the knowledge of <i>S<sub>0</sub></i>, the dynamic contrast-enhanced relaxation rate <i>R<sub>1</sub>(t)</i> is computed. +Finally, the concentration is calculated by inverting the linear model: +<i>R<sub>1</sub>(t)=R<sub>10</sub>+r<sub>1</sub>*C(t)</i>. +- <i>Turbo FLASH Sequence</i>: The conversion from signal <i>S(t)</i> to contrast agent concentration <i>C(t)</i> is calculated according to the turboFLASH (ultrafast gradient echo) sequence specific formula. \section org_mitk_views_pharmacokinetics_concentration_mri_T2_conversion Conversion of T2-weighted MRI data \imageMacro{concentration_curve_converter_T2_weighted.png,"Example screenshot of the conversion of T2-weighted MR images",3.0} -The contrast agent concentration <i>c</i> is calculated according to the formula: <i>c = -k/TE*ln(S(t)/S(0))</i>, where <i>S(t)</i> is the dynamic T2-weighted signal intensity, <i>S(0)</i> the baseline signal, <i>k</i> a user-defined conversion factor and <i>TE</i> the echo time of the employed sequence. +The dynamic contrast agent concentration <i>C(t)</i> is calculated according to the formula: <i>C(t) = -k/TE*ln(S(t)/S<sub>BL</sub>)</i>, where <i>S(t)</i> is the dynamic T2-weighted signal intensity, <i>S<sub>BL</sub></i> the baseline signal, <i>k</i> a user-defined conversion factor and <i>TE</i> the echo time of the employed sequence. In practice, the factor <i>k</i> is often set to unity. +\section org_mitk_views_pharmacokinetics_concentration_mri_lit References/Literature +- \anchor org_mitk_views_pharmacokinetics_concentration_mri_lit_ref1 [1] Wang, H. Z., Riederer, S. J., and Lee, J. N. (1987). Optimization the +precision in T1 relaxation estimation using limited flip angles. Magn Reson Med, +5:399–416. + + + */ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png index ef521cc592..6de9b777c8 100644 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png and b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T1_weighted4D.png differ diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png index cd4158f49d..91e1b6cdc8 100644 Binary files a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png and b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/documentation/UserManual/concentration_curve_converter_T2_weighted.png differ