Inobitec DICOM Viewer

2.16. Perfusion Parameters Estimation

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Functionality is available in the Pro edition
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PIC This function cannot be used for establishing a diagnosis

The following series are suitable for perfusion parameters estimation:

  • multiphase MR series. The minimal recommended phase number for brain perfusion parameters estimation is 40

  • multiphase CT series

2.16.1 Open series in Perfusion Parameters Estimation mode

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Functionality is available in the Pro edition
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PIC This function cannot be used for establishing a diagnosis

To open series in perfusion parameters estimation mode:

  1. Open a series in the View Flat Images window.

  2. Make sure that the series images are sorted by image position and phase (For details on how to sort images see Section 2.1).

  3. Select the main menu Image and the Perfusion item.

The perfusion parameters estimation panel will be displayed on the right side of the window (Fig. 2.20)

This panel has two tabs: General and Brain perfusion. The General tab allows for evaluation of the parameters of general perfusion analysis for different types of tissue. The Brain perfusion tab is used for evaluation of the perfusion analysis parameters for brain tissue.



If the series is not suitable for Perfusion Parameters Estimation, then the The current series don‘t fit in perfusion message will be displayed on the Perfusion Parameters Estimation panel.

2.16.2 Brain Perfusion Parameters Estimation

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Functionality is available in the Pro edition
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PIC This function cannot be used for establishing a diagnosis

To estimate brain perfusion parameters, go to the Brain perfusion tab.

To add a simulated artery input function (AIF), proceed as follows:

  1. Click the Add AIF. To create a simulated AIF, choose Simulated in the drop-down list.

  2. Provide the following AIF parameters:

    • Appearance time (time before the commencement of the first bolus passage);

    • Time to concentration peak;

    • Concentration peak value;

    • Sharpness.

The chart shows a simulated AIF built on the basis of the stated parameters.

Click OK to create a simulated AIF or Cancel to cancel.

To create an AIF with the help of ROI:

  1. Find the image that shows the artery.

  2. Provide the pixels intensity range in the Range of intensities section of the General tab. The range of intensities shows which pixels will be factored into the calculation and which will be neglected. A pixel is neglected if none of the values in its intensity distribution graph built by phases falls within this range. If the ROI does not contain any pixels falling within this range, no graph will be built for this ROI.

  3. Click the Add AIF button, and choose ROI in the drop-down list.

  4. Activate one of the following tools — ROI rectangle PIC , ROI ellipse PIC or ROI polygon PIC  — on the perfusion parameters estimation panel with the left, right, or middle mouse button. To continue work with the same tool, use the button with which the tool was activated. For details on tool management, see Section 1.14.

  5. Build ROI around the artery. Graphs of artery input fucntion for each ROI pixel will be displayed at the bottom of the Perfusion Parameters Estimation panel.

  6. To build an AIF, highlight several pixel graphs in ROI. To do that, select the graphs by left-clicking on them while holding the Ctrl key, or else you can move the mouse while holding the left mouse button. All the pixel graphs are highlighted by default. If you change the ROI, the selected pixel graphs will be reset. Click OK to build an AIF on the basis of the ROI, or Cancel to cancel.

  7. To limit the interval of the phases for which the parameters are calculated, enter the numbers of the first and the last phase in the respective fields, and press Enter key on the keyboard. You may also move the interval limits on the chart. To do that, pause the mouse pointer on the limit so that it appears as PIC and move the limit while holding the left mouse button.

  8. If the peak on the intensity graph is negative, you need to switch the Type of images to T2-weighted (the default value). The other value is T1-weighted. The Type of images setting is only used for MPT study series.

The AIF added will be displayed on the AIF list panel. If the AIF is based on a complete model, its name will start with the word «Simulated», if it is created with the help of ROI, its name will start with «ROI». To choose a name for an AIF, left-click the input box and print the name. All the AIF graphs are shown in dotted line. To apply a certain AIF, click on the respective AIF switch. To show or hide a certain AIF, check or uncheck the Show box. To change the pixels selected in ROI, click PIC Settings for the respective AIF. To go to the image for which the AIF was created, click PIC on the right-hand side of the name. To delete the selected AIF, click the PIC Delete button.

The charts may show:

  • The intensity values (for AIF with ROI, tissue ROI);

  • The concentration values (for all the AIF, tissue ROI);

  • The response function values (for tissue ROI).

Select Intensity, Concentration, or Response in the drop-down list over the chart. The Response chart is built for tissue ROI on the basis of the data for the AIF selected.

The X-axis shows the time, while the Y-axis shows the intensity, concentration, or the response time (depends on the chart selected).

To move the chart along the vertical axis, move the mouse up or down while holding the left mouse button and the Shift key. To resize the chart, move the mouse up or down while holding the left mouse button and the Ctrl key. If you check the Fit to plot box, the graph will be fitted to the window size. This box is checked by default. If you check the Show label box, the values will be shown in the point where the cursor is placed. This box is also checked by default.

The concentration graph for ROI objects has the following key points:

  • The point showing the commencement of the bolus passage through the tissue ROI (a round point);

  • The point showing the bolus peak concentration in the tissue ROI (a round point);

  • The point showing the end of the first bolus passage through the tissue ROI (a round point);

  • The point showing the steepest slope of the concentration curve (a square point).



To build a ROI for evaluating the intensity, concentration, or response values, proceed as follows:

  1. Activate one of the following tools — Point value PIC , ROI rectangle PIC , ROI ellipse PIC , or ROI polygon PIC  — with the left, right or middle mouse button. To continue work with the same tool, use the button with which the tool was activated. For details on tool management, see Section 1.14.

  2. Build a ROI object for the area you need.

The ROI built will be shown on the Tissue ROI list.

At the top of the perfusion parameters estimation panel, the graphs depicting the changes in intensity, concentration, or response values across time are shown. These graphs are presented as a solid line. To switch between the Intensity, Concentration, and Response parameters, choose the value you need from the Chart name drop-down list.

You may perform the following actions with the study subjects (AIF with ROI, simulated AIF, or tissue ROI):

  1. Rename.

  2. Change a color. Click the color button to the right of the AIF or ROI name.

  3. Change visibility. To make an AIF or ROI invisible, uncheck the box for the selected AIF or ROI.

  4. Move the phases. If the patient moves while scanning is being performed, the tissues for which AIF and ROI are to be built are displaced, and the phases are changed. The DICOM Viewer provides an opportunity to build AIF and ROI separately for each phase. To move an AIF or ROI for the current phase, hold down the Ctrl key while moving; for the current and all the following phases hold down the Shift key; for the current and all the previous phases hold down the Alt key. You cannot resize the ROI for a particular phase. If you try to resize the ROI for a particular phase or phase subset, the ROI for the other phases will be resized accordingly. Tissue ROI resizing and relocation only affects the evaluation of the parameters of the selected tissue area.

  5. Move to the next slice. To move an AIF or ROI to the next slice, choose Move ROI to previous slice or Move ROI to next slice in the right-click menu.

  6. Remove. Click the PIC button for selected AIF or ROI.

To go to image containing AIF or ROI, click the PIC button.

The values of the following parameters are shown for ROIs:

  • Time to peak (TTP);

  • Cerebral blood flow (CBF);

  • Cerebral blood volume (CBV);

  • Time to peak of response (Tmax);

  • Mean transit time (MTT).

2.16.3 Map mode

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Functionality is available in the Pro edition
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PIC This function cannot be used for establishing a diagnosis

To activate the map display mode, check the Enable map box on the Map tab of the perfusion panel. This box is unchecked by default.



Select one of the following parameters to show map from the Parameter dropdown menu.

For Brain perfusion tab:

  • Time to peak;

  • Area under curve;

  • Maximal slope;

  • Time to peak of response;

  • Cerebral blood volume;

  • Cerebral blood flow;

  • Mean transit time.

For General tab:

  • Time to peak;

  • Area under curve;

  • Maximal slope.

The following parameters are provided for a map:

  • CLUTs. A drop-down list of color tables that determine the map color spectrum. The [WL]Map(spectrum) color table is used by default. Users may create their own color tables with the Perfusion tag. The user’s color tables are added to the drop-down list.

  • The Range of values table is used for setting the minimum and maximum map values.
    If the Automatic selection box is checked, the input fields for the minimum and the maximum map value percentile ranks are displayed. The minimum percentile rank determines the percentage of pixels for which the parameter value is above the minimum range value. The maximum percentile rank determines the percentage of pixels for which the parameter value is below the maximum range value. When the percentile ranks are set, the entered values are checked. The value range for each field is from 1 to 100. The sum of the minimum and the maximum percentile ranks must be more than 100. If the entered value is invalid, then after you press Enter key on the keyboard, the previous valid value will be restored.
    If the Automatic selection box is unchecked, the input fields for the minimum and the maximum map values are displayed. The minimum and the maximum map values are shown at the beginning and the end of the color range. By default, the Automatic selection box is checked, with both percentile ranks at 95%.

  • Opacity. By moving the slider, you can set the map opacity.

When the map is activated, in the left-hand side of the window you see a color range (Fig. 2.23).



To hide the range, uncheck the Show color range box on the Range of values panel. This box is checked by default.

To change the range values, move your mouse over the upper or the lower bound, so that it looks like PIC . Then move the bound outwards to enlarge the range or inwards to shrink it. The bound value will be displayed when moved. When you release the mouse button, the range will be adjusted and the range values will be saved. The Automatic selection box on the Range of values panel will be unchecked. In the input fields, you will see the minimum and the maximum color range values.

The range is a separate design element and is not linked to the window. The range can be moved around the screen with the mouse, when the left button is pressed.

2.16.4 Deconvolution Advanced Settings

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Functionality is available in the Pro edition
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PIC This function cannot be used for establishing a diagnosis

To choose a deconvolution algorithm on the basis of singular value decomposition (SVD) and set its parameters, go to the Advanced tab on the perfusion panel.



To apply one of the SVD deconvolution algorithms and set its parameters, click the respective option:

  • sSVD: a non-circular algorithm. The regularization method is TSVD, the parameters adjustment method is Stationary. The threshold (the default value of 0.2) is provided as the numeric parameter.

  • cSVD: a circular algorithm. The regularization method is TSVD, the parameters adjustment method is Stationary. The threshold (the default value of 0.2) is provided as the numeric parameter.

  • oSVD: a circular algorithm. The regularization method is TSVD, the parameters adjustment method is the oscillation index. The oscillation index (the default value of 0.05) is provided as the numeric parameter.

  • Custom SVD allows for setting individual combinations of regularization methods, parameters adjustment methods, and their values.

The standard sSVD algorithm is used by default.

To choose a circular custom algorithm, check the Circular box. This box is unchecked by default.

In the Regularization method drop-down list, choose the regularization method: TSVD or Tikhonov regularization. In the Parameters adjustment method drop-down list, choose the adjustment method: Fixed or Oscillation method. The threshold value or the oscillation index depends on the chosen parameters adjustment method. If you do not know what value should be provided, leave the default value. If you change the deconvolution settings, the perfusion parameters (CBV, CBF, Tmax, MTT) will be re-evaluated for tissue ROI and maps.

To enable AIF smoothing, check the Fit the AIF data with the gamma-variate function box. If you enable the smoothing function, the ROI and AIF graphs will be smoothed. Besides, the TTP, CBV, CBF, MTT, and Tmax parameters for ROI and maps will be re-evaluated. Simulated AIFs are not smoothed as they are initially built with the help of the gamma-variate function.

To enable the smoothing of concentration charts, check the Fit the AIF tissue concentration data with the gamma-variate function box. If you enable this function, all the concentration graphs for tissue ROI will be smoothed. Besides, the TTP, CBV, CBF, MTT, and Tmax parameters for ROI and maps will be re-evaluated.

In most cases, if you enable AIF or concentration graphs smoothing, it does not affect the TTP parameter value.