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Tutorial – Visualization and Interaction

Please note that this tutorial is for the latest released nordicBrainEx. If you are using an older version please upgrade.

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m a k i n g f u n c t i o n a l M R I e a s y

nordicBrainEx Tutorial – Visualization and Interaction

Date modified: 2019-02-25 of 33

Contents 1 Coregistration ..................................................................................................................................................... 3

1.1 Inter-modality coregistration ..................................................................................................................... 3

1.2 Motion correction (BOLD/DTI/DSC/DCE) ................................................................................................... 5

1.3 Eddy current correction (DTI) ..................................................................................................................... 5

2 Visualization panels and thumbnails .................................................................................................................. 6

2.1 The menu .................................................................................................................................................... 6

2.2 Interacting with the 2D MPR views ............................................................................................................ 6

2.2.1 Overlays and palette scale information ........................................................................................... 10

2.3 The slice editor ......................................................................................................................................... 11

2.4 Interacting with the 3D viewer ................................................................................................................. 14

2.5 Interacting with the thumbnails ............................................................................................................... 18

3 Volume–of–Interest (VOI) ................................................................................................................................ 21

3.1 Creating VOIs ............................................................................................................................................ 21

3.2 Modifying VOIs ......................................................................................................................................... 23

3.3 VOI functionality ....................................................................................................................................... 24

3.4 Using VOIs with DTI fiber tracking ............................................................................................................ 25

3.5 VOI statitics ............................................................................................................................................... 26

3.6 Creating time–intensity curves................................................................................................................. 27

3.6.1 Using the scatter VOI to inspect time–intensity curves ................................................................... 28

3.7 Creating histograms ................................................................................................................................. 29

4 Report ............................................................................................................................................................... 30

4.1 Global report functions ............................................................................................................................ 30

4.2 Report element functions ........................................................................................................................ 32



1 Coregistration

1.1 Inter-modality coregistration

Automatic inter-modality coregistration uses a mutual information based algorithm to search an optimal rigid

transformation that aligns the two datasets. The implementation is based on an article by H. Sundar et al. (Sundar

et al. MICCAI. 2007. 10(Pt 1):950-8).

Coregistration is turned on/off in the Settings menu. If turned on, then after loading of datasets have completed

nordicBrainEx checks if the image series are already coregistered. The functional image series are coregistered

against the structural image series. If they are, nordicBrainEx asks if the coregistration should be done over again.

If the user chooses to redo the coregistration or if the image series has not already been coregistered against the

structural series, automatic coregistration is started. When the coregistration is finished the user is notified that

the coregistration result needs to be verified.

In the interaction panel the icons of the two image series that are coregistered against each other appear along

with a Please verify coreg button. To start the verification process press this button.

Figure 1: Redo coregistration?

Figure 2: Automatic coregistration is finished.

Figure 3: Verify the coregistration.



The image series that is coregistered against the structural series will be shown as an overlay on the structural

image series, enabling a visual inspection of the coregistration.

In Figure 4 the tools for adjusting and visualizing the coregistration result are shown. You can change the opacity

of the overlay, switch to another overlay palette, or use a checker board visualization.

At the top of this panel are the controls for interaction with the coregistration.

There are basically three options:

• Verify the automatic coregistration results

If the results of the automatic coregistration are acceptable, then verify the results by clicking on Verify

button.

• Manually coregister the data

If manual adjustments are necessary click on the two Manual coregistration buttons (or press Ctrl+t/Ctrl+r)

in order to enable manual translation and/or rotation. When these modes are enabled you can

interactively adjust the overlaid dataset to align with the structural by using your mouse. Alternatively you

alter the translations and rotations by manually changing the coregistration parameters. The MPR-

crosshair can be helpful during visual inspection and can be toggle on/off using the checkbox.

• Restart coregistration

Click on Redo button to restart automatic coregistration. The algorithm will start the search for a good

match from the present coregistration settings. If you check the Use Brain Extraction option, the image

Figure 4: Working with the coregistration.



series will be brain extracted before the coregistration is started. This might in some cases give a better

result.

You have to verify the coregistration first before the analysis of BOLD, DTI, or DSC data starts.

1.2 Motion correction (BOLD/DTI/DSC/DCE)

The motion correction is an optional preprocessing step in the BOLD, DTI, DSC and DCE analysis that you can tick

off in the respective settings interface, see sections ‘DSC settings’ in ‘Tutorial DSC’, ‘DCE settings’ in ‘Tutorial DCE’,

‘BOLD design files’ in ‘Tutorial – BOLD’, and ‘DTI settings’ in ‘Tutorial – DTI’. For each source volume the rotation

and translation parameters are estimated, in an iterative manner, with regards to the first volume which is the

reference volume. These parameters are saved internally so that the user can display them at a later stage by right-

clicking on the icon of the dynamic series and choose Motion Correction Results.

Because of the optimization nature of these algorithms, for certain datasets it may result in local, incorrect, minima

that are indistinguishable from the ‘true’ global minimum. Therefore, it is recommended to inspect the motion

correction results for any obvious misalignments.

1.3 Eddy current correction (DTI)

The Eddy current correction is an optional preprocessing step in DTI analysis, see section ‘Details on configuring

DTI settings’ in ‘Tutorial – DTI’. The transformation model used in motion and eddy current correction of diffusion

weighted images is based on an article published in 2004 by Rohde et al. Magn. Reson. Med. 2004.51:103-–114.

Certain approximations of the deformations due to Eddy currents allows us to describe the transformation as

x = MDx’

mapping a voxel x’ from the distorted diffusion weighted volume space to the undistorted space of the reference

volume. M is the rigid transformation matrix, while D written out is

(

1𝑐1 𝑐2 𝑐3

11

)

where c1, c2 and c3 are the first order terms (from Eddy current artifacts) mentioned in Rohde's article. The

optimization method is based on an article from 2001 by T. Netsch et al. titled Towards real-time multi-modality

3D medical image registration, which uses local correlation as the cost function.



2 Visualization panels and thumbnails

2.1 The menu

File

Use this menu to open the database or save the session.

Settings

• Synchronize 3D and MPR view. If ticked on, the position of the crosshair / planes in MPR and 3D viewer

are synchronized.

• Export results as… This setting will decide which export format that is used for BOLD/DTI/DSC/DCE results

that are to be exported into neuronavigation systems.

• Smooth fibers on export. If ticked on, this will smooth the DTI fiber group before it is merged into the

structural series/geometry for export to neuronavigation systems. This smoothing will also apply to DTI

fiber groups displayed in MPR. Turning the smoothing off will increase the speed of ‘Merge’ and ‘View in

MPR’ in the DTI interaction tab.

• Limit displayed resolution in MPR. If the user experiences problems with the application running out of

memory, limit the displayed resolution in the MPR can help mitigate this problem. The data will then be

resampled into the chosen resolution. Note that only the displayed resolution in MPR is reduced, and this

will affect any ‘Create snapshot’ / ‘Slice selection’ / and “Slice all’ outputs created, but not any merged

output maps. Merged series will keep the original resolution.

• Use coregistration. If this is not checked, the analysis will be done without coregistrating / aligning the

different series to the structural underlay. Using coregistration is recommended.

2.2 Interacting with the 2D MPR views

The 2D Multiplanar Reconstruction (MPR) views display one underlay volume which can have several overlays.

There are multiple interaction options available for the 2D MPR views which you can access by right–clicking one

of the 2D MPR views or one of the thumbnails in the data panel. We will go through these options in detail in this

section. In addition to right-clicking you can also interact with the 2D MPR views using the mouse in the following

way:

• Left–clicking one of the 2D MPR views will move the two other MPR views to visualize the point in the

brain were you clicked. You can also move around by holding the left mouse key down and move the

mouse over the image.

• Holding down the middle mouse key while moving the mouse over the image will change the window level

and the window width (described below).

• If your mouse has a wheel and you roll it over one of the 2D MPR views that plane will be moved slice by

slice through the brain.



Note that these interactions in the 2D MPR views also can update the 3D viewer. Go to File -> Settings and check

Synchronize 3D and MPR view if you want the 3D viewer to be synchronized with the 2D MPR.

Right–clicking one of the 2D MPR views will give you the following options:

• Acquisition parameters

Display patient and dataset information in the 2D MPR views (see Figure 5).

• Add distance measure tool

Add a distance measure tool to the current view (see Figure 5).

• Remove all distance measure tools

Remove all distance measure tools that have been added.

• Slice selection

Figure 5: Interaction options in the 2D multiplanar views.



Open the slice selection tool where you can select the area to slice, see Figure 6. Selecting Slice will open

the slice editor. See section 2.3 The slice editor for more deitals.

Figure 6: Slice selection in the axial view. In the axial view slices in coronal or sagittal orientation can be generated. You can flip the orientation of the selection interface by ticking off the ’Horizontal’ checkbox. If fixed width is selected, the width can be specified by the

user. Otherwise, the slice distance is generated by the number of slices and the slab thickness (the green lines).

• Slice all

Generates a set of slices that mimics the original slices of the underlay with regard to number of slices and

slice positions. Note that this equivalence only applies when this option is run from the frame in the 2D

MPR with the same orientation as the slice direction of the underlay. The slicing includes all current

overlays and VOIs present. When slicing is done you get a thumbnail under Derived data and the slice

editor window opens up where you can send and save slices (See section 2.3 The slice editor for more

deitals).

• Create snapshot

Create a snapshot of the current view. The slice editor window opens up where you can send and save the

snapshot (See section 2.3 The slice editor below for more deitals).

• Create snapshot of MPR

Create a snapshot of the MPR in the same way as for Create snapshot above.

• Copy

Start slicing



Copy the current 2D view to clipboard, you can then paste it where you want.

• Enable zoom/pan mode

Enabling zoom and pan mode will allow you to hold down the right mouse key and move the mouse to

zoom in and out, and in the same way hold the left key to pan. A miniature of the frame in the top right

corner will show you which part of the frame you are looking at, see the axial view in Figure 5. Clicking the

cross in this miniature turns off zoom/pan mode.

• Toggle window size

Toggle between showing the MPR and the 3D, and to see only the current image. This feature can also be

toggled by double–clicking in the window.

• Window level/width

Image contrast and intensity is often referred to as window width (contrast) and window level (intensity).

This information is read from the DICOM header if available. When you open the Window level/width

option you get a list of your current overlay and underlay, select the one to adjust and then click Toggle

window level. You can change both values by keeping the left or the middle mouse button down and move

the mouse in horizontal (contrast) or in vertical (intensity) direction on top of one of the 2D MPR views,

or you can type in a particular value for maximum or minimum. The current window level and window

width is shown in the MPR views (see Figure 7). Right-click to finish.

Figure 7: A CBV map is added as an overlay, and toggle window level for CBV has been selected. On the right, the minimum value has been increased to exclude the lowest values from the visualization. Note that for a CBV map, this can also be done using the CBV thresholding in the DSC tab.

• Interpolation of underlay

Toggle interpolation of the underlay on/off. A checkbox will indicate whether interpolation is turned on or

off.

• Interpolation of overlay

Toggle interpolation of the overlay. A checkbox will indicate whether interpolation is turned on or off.



2.2.1 Overlays and palette scale information

Overlays will be displayed with a palette/color scale. The palette scale will only be displayed when one overlay is

shown, i.e. the following applies:

• The palette scale will be displayed if one overlay is added but will be removed if more than one overlay is

added.

• If BOLD analysis is done, the palette scale will be displayed if one BOLD contrast is selected, but not if

more than one contrast is selected.

• If BOLD overlays are combined with other overlays, no palette scale will be displayed.

To display the palette scale, simply select to display one overlay at the time.

The numerical pixel value mappings for the palette scale will be visible when hovering the mouse pointer over

the scale.

If several overlays use the same palette, it will not be possible to add to create a slice package (see next section).

This is to avoid confusion when several overlays look similar. This also applies to situations where one of the

overlays is a BOLD contrast (e.g. if a BOLD contrast with the hot palette is combined with an overlay with the

same hot palette).

The max and min values for the scale are included in the slice packages.



2.3 The slice editor

Figure 8: The slice editor displays the slice package selected in the MPR through slice all / slice selection or create snapshot. In the example in this figure, a study with perfusion is loaded, and the CBV map is displayed as overlays. Two VOIs have been created, their statistical values have been displayed, as well as histogram for CBV and DSC time curves for the two VOIs. This information is displayed together with the slice package and can be saved to PACS.



The purpose of the slice editor (Figure 8 and Figure 9) is to allow for easy saving of results to PACS or other

remote entities. The output is a derived series without geometry, showing components from the MPR and any

interactions (overlays, VOIs and VOI statistics, histograms, intensity curves, BOLD threshold etc.).

The slice editor will display the slice / slice package as defined by the slice all / slice selection or create snapshot

from MPR. The following options are available:

• Close: Will close the slice editor. The series will be saved as a thumbnail, but not saved automatically.

The thumbnail can be saved manually later.

• Save and send: will save the slice package to the database as a new derived series and open a dialog box

with the defined remote entities for sending of the series to PACS.

• Save to database: will save the series to the local database only.

• Orientation images: will display the current position of the main orientation by crosshairs/lines on the

two other orientations. In the example above, the position of the axial slice is indicated as a blue line on

the coronal and sagittal views. The line with the slice position will automatically updates when scrolling

through the slices. Per default, the orientation images are displayed.

• Cross hair: Enable if you want crosshair to show in the main frame.

• BOLD activation info: If any BOLD activation maps are present, this will display the current BOLD T-/P-

value of the selected BOLD activation maps as displayed in MPR. Per default, the BOLD activation info is

displayed.

• VOI statistics: If any VOIs have been created in the MPR, and the VOI statistics for those VOIs have been

selected in the interaction and visualization panel, this will display the statistical information from the

selected VOIs. Per default, VOI statistics is displayed.

• Histogram: If any VOIs have been created in the MPR, and the histogram for those VOIs have been

selected in the interaction and visualization panel, this will display the histogram from the selected VOIs.

Per default, histograms are displayed if they exist.

• Intensity Curves: If any VOIs have been created in the MPR, and the intensity curves for those VOIs have

been selected in the interaction and visualization panel, this will display the intensity curves from the

selected VOIs. Per default, intensity curves are displayed if they exist.



Figure 9: The slice editor displays the slice package selected in the MPR through slice all / slice selection or create snapshot. In the example in this figure, a study with BOLD and one contrast is analyzed. One overlay VOI of the BOLD activation has been created, and the statistical values for the BOLD activations (the overlay VOI) is displayed as intensity curves. This information is displayed together with the slice package and can be saved to PACS.



2.4 Interacting with the 3D viewer

The 3D viewing window enables visualization of the white matter fiber tracts as output from the DTI analysis. It

can also be combined with BOLD activations by rendering the activations as 3D blobs.

The 3D viewing window in nordicBrainEx is illustrated in Figure 10. There are various features and controls

embedded within the window for manipulating the current view:

• Fiber opacity

Move the mouse over this text field located in the top row of the window to display a slider that can be

used to change the opacity (transparency) of the visualized fibers. Note that using reduced opacity on

interleaved objects like fiber-tracts might cause object to be visualized wrong with regards to what objects

are visualized in front of what objects.

• Plane opacity

Move the mouse over this text field located in the top row of the window to display a slider that can be

used to change the opacity (transparency) of the image planes. Note that using reduced opacity on

interleaved objects might cause object like planes to be visualized wrong with regards to what objects are

visualized in front of what objects in different areas.

• AXIAL/CORONAL/SAGITTAL

Figure 10: Interaction options in the 3D window in nordicBrainEx.



Move the mouse over any of these words located in the bottom row of the window to display a slider that

can be used to scroll through the slices of the image volume.

• 3D Options

Move the mouse over this button located in the upper left corner to open the 3D options. It can also be

opened by right-clicking in the 3D window.

• Add to report

Click this button located in the bottom left corner to add a snapshot of the current view to the report, see

section ‘Report’.

The basic navigation is done by using your mouse in the following way:

• Rotation of the image volume

Hold down the left mouse key and move the mouse.

• Panning the image volume

Hold down the middle mouse key and move the mouse. Alternatively you can hold down the SHIFT button

when holding down the left mouse key.

• Zooming the image volume

Hold down the right mouse key and move the mouse up/down to zoom in/out respectively.

• Information about a tube

Hold down shift and click on a tube to get the information about it. Hold down shift and click outside the

tube to remove the information. This feature is only available if a DTI dataset has been loaded.

Right–clicking in the 3D window (or clicking the 3D Options button) will give you the following 3D options:

Figure 11: The animation tool in the 3D view.



• Toggle window size

Toggle between showing the 3D window in full–screen mode or normal view. This feature can also be

toggled by double–clicking in the window.

• Reset 3D viewer

Reset all options you have chosen in the 3D visualization. Note that all the fiber groups will be lost.

• Create snapshots/animation

Enables animation mode. Various screen–captures and animations can be created of the 3D window, see

Figure 11. Specify the amount of Rotation/Zoom using the corresponding drop–down menu and value

field, rotation values are given in degrees. Specify the number of Steps to be included in the animation.

When you create an animation a new thumbnail holding the resulting snapshots will be created under

Derived data. Right-click the thumbnail and select View slices to open the slice viewer window Figure 14).

In this window you can save the animation in the AVI format, send it to the report, save it to the database

or send it to a remote DICOM node, like e.g. a PACS system.

• Hide plane…

Toggle the visibility of any image plane (AXIAL/CORONAL/SAGITTAL).

• Reset view to...

Reset the view to any of the orientations (AXIAL/CORONAL/SAGITTAL).

• Interaction mode

Select between different interaction modes, i.e. how the view is updated during rotation/

panning/zooming. Default is Trackball.

• Plane interpolation

Toggle on/off interpolation of the visualized image planes. The interpolation uses a nearest neighbor

approach.

• Render fibers

Toggle on/off the rendering of the fibers. This option is only available if a DTI dataset has been loaded and

fiber tracking is performed.

• Hide group properties

Toggle the visibility of any fiber group properties.

• Color fibers by direction

Toggle the coloring scheme of the visualized fibers. When enabled, the fibers are colored according to

their direction (Red: Left–right, Green: Anterior–Posterior, Blue: Inferior–Superior). When disabled, the

fibers have one single color as defined by the Set fiber color... menu entry, see below.

• Set fiber color...

Set the color of the visualized fibers.

• Render fibers as tubes

Visualize fibers as thicker tubes. Note that this may reduce the performance and interactivity of the 3D

window depending on the number of fibers currently being visualized.

• Render volume

Render volume as shown in Figure 12. Note that the volume will be rendered in a cropping box and that

the basic navigation described above (using the left, middle or right mouse key) only works if you click

outside this box. By clicking inside the box you move the box itself. You can also grab the bullets in the box



to resize it. Also note that when Render volume is selected more options appear in the popup. These

options are explained below.

• Hide Orientation Box

Toggle the visibility of the orientation box located at the bottom right corner of the 3D window.

When you select the 3D option Render volume the right-click menu will give you these additional options (see

Figure 12):

• Opacity Function

Shows the window for working with the opacity transfer function.

• Ray casting

Turn on/off rendering using ray casting. Switching it off may improve performance.

• Cropping Box

Show cropping box used for cropping the dataset.

• Clipping Plane

Show a clipping plane used for clipping the dataset.

• Reset clipping/cropping

Resets all clipping and cropping done by the clipping planes and the cropping box.

• Clip/crop overlays

Toggles whether or not the clipping planes or cropping box should clip/crop through the overlay.

Unselecting this option makes overlays such as BOLD activations appear as 3D-volumes.

• Shadow overlays

Toggles the rendering option of adding shadows to the overlays on/off.

Figure 12: Render volume in the 3D window. Note that this gives you a set of new options in the popup.



2.5 Interacting with the thumbnails

Underlay and overlay datasets in the 2D and 3D multiplanar view can be changed by right–clicking the thumbnails

in the data panel. There are different options for structural and functional data which will be listed in the popup

menu that appears when you right–click the thumbnail, see Figure 13.

Right–clicking a thumbnail in the data panel will give you some of the following options:

• View as underlay

Displays the dataset which corresponds to the thumbnail as underlay in the 2D multiplanar view. Only one

of the datasets can be an underlay at the time. There must always be an underlay.

• View as overlay

Displays the dataset which corresponds to the thumbnail as overlay in the 2D multiplanar view. You can

add and remove overlays to view several, one or none overlays.

• View in 3D

Displays the dataset which corresponds to the thumbnail as underlay in the 3D viewer.

• View slices

View slices of the dataset in the slice viewer window (see Figure 14).

Figure 13: The right–click menu of the structural and functional data differs slightly.



Figure 14: The slice viewer. View dicom header: available once the derived series is saved to the local database.

• Send

Send the dataset to a remote DICOM node, like e.g. a PACS system. You need to set up remote entities to

use this functionality. Go to File -> Database -> Settings to add a remote entity (see Tutorial – Handling

Image Data for additional information). Note that you cannot send a dataset unless it is saved in the

database (if you have a derived dataset you have to save it before you can send it).

• Show dicom info

Show dicom information for the dataset. Note that this option is only available for datasets that are saved

in the database (if you have a derived dataset you have to save it before you get this option).

• View dynamic series

The dynamic series will be displayed volume–wise in the 2D MPR views. Change the displayed volume by

using the white slider in the axial view, see Figure 15.

• BOLD / DTI / DSC / DCE settings

A BOLD dataset’s thumbnail will give you the option to edit and save the settings/design file, import or

create a new design file. For a DTI, DCE or DSC dataset the settings window will open so that changes can

be made. See ‘Tutorial – BOLD’, ‘Tutorial – DTI’, ‘Tutorial – DCE’ and ‘Tutorial – DSC’ for more information

on settings.

• Spike detection

The Spike Detection window gives you the opportunity to discard slices that you find have spikes and re-

run the analysis. See section ‘Spike detection in BOLD’ in ‘Tutorial – BOLD’ and section ‘DTI spike detecion’

in ‘Tutorial – DTI’.

• Motion correction results



This option gives you a pop-window with the results from the motion correction and/or eddy current

correction graphically displayed. The results from motion correction are given in the graphs called

Translation parameters and Translation parameters, while the results from the eddy current correction

are called Deformation parameters. This option is only available for functional datasets where either

motion correction or eddy current correction was performed. See section ‘Motion correction

(BOLD/DTI/DSC/DCE).

• Remove

Remove the dataset from this session. You have to re-load it or generate it again if you want to have it

back.

Figure 15: View dynamic series enabled.



3 Volume–of–Interest (VOI)

3.1 Creating VOIs

The Volume–of–Interest (VOI) tool in nordicBrainEx encompass some of the core features in the Visualization step

as it offers comprehensive functionality for interacting with both the BOLD, DTI, DCE and DSC data. The Volume-

of-Interest section is situated in the interaction panel to the right, see Figure 16.

Figure 16: The interaction with Volume-of-Interest (VOI) tool is done on the right-hand side of the Visualization and Interaction panel (indicated with a red square).

When a VOI is added, it will be shown with a bounding box in the Multiplanar Reconstruction views and the 3D

viewer (with the exception of the Scatter VOIs). In order to add a VOI click on the button Add new VOI in the

Volume-of-Interest section (Figure 16). A drop–down menu allows you to choose the VOI type:

• Ellipsoid

Add a VOI with an ellipsoid shape. The VOI will initially be positioned at the location of the cross–hairs in

the MPR view.

• Cube

Add a VOI with a cubic shape. The VOI will initially be positioned at the location of the cross–hairs in the

MPR view.

• Polygon



Add a polygon VOI. When choosing this VOI; use your mouse to draw a polygon on one of the MPR planes;

click to add the points to the polygon. When you have finished you click the Finish button and the polygon

will be added to the list of VOIs.

• Free-hand

Add a free-hand VOI. When choosing this VOI; use your mouse to draw the VOI on one of the MPR planes.

The drawing is done by holding down the left mouse button while drawing, and the drawing is finished

when the mouse button is released.

• Scatter

Add a scatter VOI. When choosing this VOI the Create scatter VOI - tool will open, see Figure 17. By using

the slider you can move through all the slices in the current underlay’s scan orientation. Choose Brush and

click on the pixels you want to add to the VOI. You can select the pixels one by one or 9 at a time (see

Figure 17). When Eraser is chosen you can remove already selected pixels from the VOI. Before you start

to select pixels you might want to zoom in the area of interest. You can turn on/off the Zoom/Pan-mode

by clicking the Zoom/Pan button. When in Zoom/Pan-mode you can zoom by moving the mouse holding

down the right mouse key and pan by holding down the left mouse key. To start to select pixels you have

to leave Zoom/Pan-mode by clicking this button once more. When the desired set of pixels are selected

you can click Save to actually create the VOI. With the Cancel button you cancel the creation of this scatter

VOI. Note that the Create scatter VOI - tool also has a checkbox to show/hide current overlays. Only overlay

datasets that are derived from the underlay can be visualized in the tool. The checkbox to show/hide grid

will toggle a grid that will be overlaid the visualized images reflecting the inherit resolution of the dataset

and making it easier to see the actual pixel size. NOTE: This VOI type can typically be used to inspect time

intensity curves, see section ‘Creating time–intensity curves’.

Figure 17: Tool to create a scatter VOI.



3.2 Modifying VOIs

A VOI can be translated, rotated and scaled, and the MPR views and the 3D viewer will then be updated

accordingly. You can transform the VOI in three ways in the 2D MPR views:

• Translation

Translate the VOI by interacting with the red point in the middle of the shape.

• Scaling

Scale the VOI by interacting with the four yellow corner points.

• Rotation

Rotate the VOI by using the green point in the lower right corner. Rotation can only be performed in the

2D MPR views (see Figure 18).

Figure 18: Rotation of a VOI is done by moving the green dot.

In the 3D viewer the VOI is displayed inside a box with 7 interaction handles, shown as spheres. These can be used

to translate and scale the VOI (rotation is not possible in the 3D view):

• Translation in 3D viewer

Translate the VOI by clicking on the handle in the center of the box. Alternatively you can click on the

bounding box with the middle mouse button.

• Scaling in 3D viewer

Scale the VOI by interacting with the six outer handles of the box. Alternatively you can click on the

bounding box with the right mouse button to scale the box.



3.3 VOI functionality

All the added VOIs are listed in the Volume-of-Interest section (Figure 19).

Figure 19: Two VOIs are created and displayed in the Volume of interest list (left). When clicking on the color box, additional options are opened (right).

For each VOI you have a set of icons/options to interact with that specific VOI:

• Visibility checkbox for the VOI

If checked the VOI is visible in the 2D MPR views and in the 3D viewer.

• Name of the VOI

You can edit the default name of the VOI by clicking on the field and write.

• Color/visualization options

Click the color icon to open an option panel:

- Change the VOI’s color and its opacity

- Toggle whether the bounding box should be visible or not.

- Find VOI (binoculars)

By clicking the binoculars button the planes will adjust themselves so that the VOI is in the center of

the planes shown. This button can help you re-find your VOI if you have navigated away from the VOI

and can no longer see it in any of the views.

• Show/Hide VOI statitics

Click to open the VOI statistical information for the current VOI. See section ‘VOI statitics’.

• Show/Hide intensity curve

Click to open this VOI’s intensity curve for a dynamic dataset, i.e. you need to load at least one dynamic

dataset to use this option. Note that if you click this button for several VOIs their curves will all come up



in the same diagram, distinguished by their color. Right-click the diagram to add the design graph or to

add this curve to the report or save as text-file. See section ‘Creating time–intensity curves’.

• Show/Hide histogram

Click to open this VOI’s histogram. Note that if you click this button for several VOIs their histograms will

all come up in the same diagram, distinguished by their color. Right-click the diagram to add it to the report

or save to text-file. See section ‘Creating histograms’.

• Logical operator

In this dropdown you can mark the VOI with AND, OR, NOT or Seed. The section ‘Using VOIs with DTI fiber

tracking’ explains how the logical operators are used and how they are read in nordicBrainEx.

• Delete VOI

Click to delete this VOI. Click on the larger x-symbol on the top of the list to delete all VOIs.

• Create segmented VOI

Create a new VOI based on the signal level of the selected map (e.g. BOLD contrast, CBV map, FA map,

structural) inside the current VOI, i.e. the new VOI will contain all the pixels in the current VOI that is above

the BOLD threshold / window level, see Figure 20. Due to differences in resolution, the activation VOI

might not match pixel by pixel with the overlaying map.

Figure 20: How to create a segmented VOI. 1) set the BOLD threshold / window level of underlay / overlay to a desired level; 2) create a VOI (ellipsoid or cube) around the area of interest; 3) select ‘Create segmented VOI’ of the VOI created in step 2, and select the desired map from the dropdown; 4) This will turn the signal within large VOI which is above the chosen threshold / window level into a VOI. In the example above, we see that the BOLD activation is shown in pink, which is the color of the VOI. This VOI can be used further to inspect the VOI statistics, intensity curve, histogram etc. Note that in order for maps to be available for this functionality (visible in the dropdown), they have to be added as overlay. The current underlay and any BOLD contrast will always be available for this functionality.

3.4 Using VOIs with DTI fiber tracking

One or multiple VOIs can be used to explore DTI fiber connectivity between different regions in the 3D viewer or

define a Seed for narrowing down the search premises for Fiber Tracking (see ‘Tutorial – DTI’ for more details). In

order to use a VOI for fiber selection, start by creating and positioning the VOI as explained in the section ‘Creating

VOIs’. You can then mark the VOI with a logical operator from its drop–down menu with AND, OR, NOT or Seed.

If a VOI is marked with Seed it means that it is defined as a Seed region for fiber tracking. You are then asked if you

want to rerun the fiber tracking, and the Fiber Tracking search algorithm will then start from the voxels within this

VOI. Note that you will also get this question if you change a VOI to no longer be marked with Seed.



It is important to notice that the logical operators in BrainEx are read in a certain order:

1. The fibers going through all the VOIs marked with AND are selected.

2. The fibers going through one or more of the OR VOIs are added.

3. The fibers going through one or more of the NOT VOIs are excluded.

Note: with no logical operators on your VOIs, all the fibers are shown. Adding an AND to one VOI will remove all

the fibers that don’t go through that VOI. If you have no logical operators (all fibers are shown) and then add an

OR to one of your VOIs then nothing happens. This is because OR only adds all the fibers inside it to the selection

you already have (in this case: all fibers).

When a VOI with an assigned AND/OR/NOT attribute is moved/scaled/resized, the fiber view will be updated to

reflect the changes.

3.5 VOI statitics

When VOIs are created, the VOI statistical information can be displayed on a list, by selecting the VOI statistics

button next to the VOI (the ‘i’). The ‘i’ must be selected for all VOIs where the VOI statistics is to be displayed.

Figure 21: The VOI statistics of the two VOIs are displayed by selecting the ‘i’ next to the VOI name and color indicator box.

Series to be displayed in the list is selected from the Select datasets dropdown. By default, the overlay that was

added last is the default selection in the list. Any structural source data and any derived map can be displayed, and

multiple maps from multiple VOIs can be displayed simultaneously, as shown in Figure 22. Dynamic source data

are not available.



Figure 22: Any derived map is available from the VOI statistics dropdown list. Here, nCBV and nCBF from perfusion analysis, and ADC from DTI analysis from two different VOIs are listed.

The list can be saved to text-file by right-clicking on the list. Additionally, the VOI statistical information can be

displayed on slice packages that are saved to PACS using Create snapshot, Slice selection or Slice all in the MPR

(see Figure 8).

3.6 Creating time–intensity curves

You can use the VOI tool to inspect the time–intensity curves for dynamic datasets. This allows you to visualize the

dynamic signal in a BOLD, DTI, DCE or DSC dataset.

In order to create a time–intensity curve start by creating and positioning a VOI as explained in section ‘Creating

VOIs’. You can then create a curve for this VOI by clicking on the time–intensity curve symbol next to the VOI, see

Figure 23.

Figure 23: Intensity curves can be displayed by clicking on the intensity curve symbol in the VOI list.

This will display the intensity curve in the lower right panel. If you have loaded more than one dynamic series, a

drop–down menu enables you to choose the series you want to see the time intensity curve for. If you right-click

on the diagram you get the option to add the design graph (BOLD only, see Figure 24, left), save to text-file or add

curve to the report. Intensity curves from multiple VOIs can be displayed simultaneously, as shown in Figure 24

(right).



Figure 24: Left: the intensity curve (time curve) of a BOLD activation (VOI created by selecting an overlay VOI of the BOLD signal as explained in Modifying VOIs). The BOLD design graph can be displayed by right-clicking. Right: Intensity curves from a perfusion series from

two different regions (VOIs).

Whenever the VOI is moved/scaled/resized the curve will be updated to reflect the signal curve in the current VOI.

3.6.1 Using the scatter VOI to inspect time–intensity curves

The scatter VOI type has some additional features compared to other VOI types that allows interactive inspection

of time–intensity curves within individual pixels. This can be done by following these steps:

1. Right–click on the thumbnail (in the data panel to the left) of the dynamic dataset to be inspected and

select View as underlay. This will change the current visualized volume in the MPR views to the first volume

of the dynamic dataset.

Figure 25: Tool to create a scatter VOI: a dynamic dataset is selected as underlay and therefore the time–intensity curves at the current mouse position is visualized. In the above example, a BOLD dynamic series is selected as an underlay. This can also be used to investigate

the time curves of a perfusion series.



2. Add a scatter VOI as explained in the section ‘Creating VOIs’ on page 21. This time when the tool to create

a scatter VOI opens (Figure 17) it will also show the time–intensity curves for each of the pixels in a 33–

matrix (Figure 25). The reason for this is that a dynamic dataset is selected as underlay.

3. Move the mouse over one of the pixels. That pixel’s intensity curve is the green curve in the middle of the

matrix, and its adjacent pixels have their intensity curves shown in red around it (see Figure 25). The 3

3–matrix of time–intensity curves will update to always show the curves at the current mouse position.

4. You can use the Zoom/Pan-mode as described in section ‘Creating VOIs’ on page 21. If you want to create

a scatter VOI and not only investigate the time–intensity curves for the pixels use the buttons and options

above the curves (they are all described in the section ‘Creating VOIs’ on page 21).

3.7 Creating histograms

You can also use a VOI to create histograms of various parametric values. In order to create a histogram, start by

creating and positioning a VOI as explained in section ‘Creating VOIs’ on page 21. You can then open its histogram

by clicking on the histogram symbol for that VOI in the list, see Figure 26.

Figure 26: The histogram can be displayed by clicking on the histogram symbol in the VOI list.

The histogram will open in the lower right panel and a drop–down menu enables you to choose which dataset

should be used as the source data for the curve. Whenever the VOI is moved/scaled/resized the histogram will be

updated to reflect the signal curve in the current VOI. If you want to add the histogram to the report you right-

click on the histogram and select Add histogram to report. The histogram can also be saved as a text file by right-

clicking on the histogram.

Figure 27: Histograms from two VOIs on a normalized CBV map are shown. In this example, the two VOIs are measuring the signal in the normal tissue and tumor tissue, illustrating an increased CBV in the tumor tissue (see Figure 21).



4 Report

4.1 Global report functions

The nordicBrainEx report module provides tools for generating a report based on the analysis results. The report

can include screenshots from the visualization step, in addition to text, headlines and an appendix which is a

summary of the image data that were used and the analysis that has been performed. You can go back and forth

between the visualization view and the report by using the navigation buttons in the upper right corner of

nordicBrainEx.

If you start nordicBrainEx and load new patient data an empty report will be opened, only containing information

about the patient that is automatically extracted from the image. You can add images, text and an appendix to this

report, or you can open an existing report. You can only open an existing report for the same patient. You can also

create a new report. Note that if you open a saved session you will get the report that was saved in that session.

Figure 28: The report interface in nordicBrainEx.



All buttons on top of the report preview (Figure 28) are global report functions. The available buttons are shown

in Figure 29 and gives you the following features:

• Back

Go to the previous page of the report.

• Next

Go to the next page of the report.

• Zoom in

Zoom in the report preview.

• Zoom out

Zoom out the report preview.

• New

Create a new report. You are informed that you will lose the current report if you have not saved it.

• Open

Open an existing report which was saved in the nordicBrainEx report format. It is only possible to open

reports that have been generated for the same patient, whose image data are currently opened.

• Save

Save the report as a pdf file, a DICOM file or a nordicBrainEx report. A nordicBrainEx report can be re–

opened and modified later on. Note that when you save a session the report you are currently working on

will be saved and re-opened when you re-load that session.

• Save to database

Save the report to the database. You will not be able to modify the report afterwards, you can only save

additional reports to the database.

• Refresh

Refresh the report preview.

• Print

Print the current report.

• Printer settings

Define settings for your local printer.

Figure 29: Interaction buttons on top of the report preview.



4.2 Report element functions

You can add different types of elements to the report: image, text, graph, appendix etc. When an element is added

it will show up in the tree structure (Figure 28). In order to modify elements, e.g. edit the text or scale images,

choose the element you want to modify in the tree structure. Its interaction tab will then open so that you can

interact with that report element. Note that some of the nodes in the tree can be opened to see/select their

subnodes. If you want to change the order of report elements you select an element that you want to move up or

down in the tree structure and click on the Up and Down button (described below).

If you want to add a text component to the report click the Add text button described below, and then click on the

text component that appears in the tree structure. This will open the text interaction tab where you can edit the

text. The result will be displayed in the Report preview.

Graphs can be added by right clicking on them and select Add to report, e.g. histogram and intensity curves for

VOIs (described in section ‘Modifying VOIs’).

Screenshots can be added to the report by clicking on Add to report in the lower left corner of each visualization

view, see Figure 30. You can also add images when you have performed slicing by clicking on the Report buttons

in the slice viewer window (see Figure 14). When an image is added you can select it in the tree structure to open

it in the interaction tab below. In the interaction tab you can then scale the image, give it a name and add markers

(circle or arrow). To edit the text for the marker select the marker in the tree structure and write in the Edit field

in the interaction tab. You can also change the color or shape of the marker at any time by selecting it and then

click Edit marker in the interaction tab.



You can add an appendix to the end of the report by clicking on the Add appendix button. This will summarize

which image data were used and which analysis steps were performed. If motion correction and/or eddy current

correction was performed the results will be displayed as graphs in the appendix.

The buttons above the tree structure in Figure 28 are used to interact with the components in the tree structure.

The available functions are:

• Navigation

Up and Down buttons for changing the order of the elements in the report, e.g. select an element in the

three structure and click the Up button will make this element raise above the element above it.

• Add text

A text component will be added to the report. You can also choose to enter a headline.

• Add appendix

The appendix adds a summary of the image acquisition parameters and of the analysis that has been

performed at the end of the report.

• Delete element

You can at any time delete an element from the report: text, images, markers etc. Select the element you

wish to delete and then click the Delete element button.

Figure 30: Adding a screenshot by clicking on ’Add to report’ in the MPR views and the 3D viewer.

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