Stroke Quantification Tool (Sonia) Ver User Manual

Transcription

1 Stroke Quantification Tool (Sonia) Ver. 1.0 User Manual English. 12/2016 Rev

2 Table of Contents 1. Introduction Installation Data Import Registration Diffusion Parameters Brain Segmentation Quantification Preferences

3 1. Introduction WAKE-UP is a European multicentre investigator-initiated randomized placebo-controlled clinical trial of MRI based thrombolysis in acute stroke patients with unknown time of symptom onset, e.g. due to recognition of stroke symptoms on awakening. Stroke is a devastating disease leading to death and disability in large numbers of patients with massive social and economic impact. Intravenous thrombolysis with Alteplase is available as effective and safe treatment of acute stroke within 4.5 hours of symptom onset. However, in about 20% of acute stroke patients time of symptom onset is unknown e.g. because symptoms are recognized when waking-up from sleep in the morning. This large group of patients is currently excluded from treatment with Alteplase only due to the missing information on the time of symptom onset. In preparatory work the WAKE-UP consortium has developed an innovative approach of using brain MRI as surrogate marker of stroke lesion age which may be used to identify stroke patients likely to benefit from thrombolysis. The objective of WAKE-UP is to test efficacy and safety of MRI-based intravenous thrombolysis with Alteplase in patients waking up with stroke symptoms or patients with unknown symptom onset. By this, WAKE-UP aims at providing a new safe and effective treatment option for acute stroke patients waking up with stroke symptoms. The project is centrally coordinated by the Universitätsklinikum Hamburg-Eppendorf (Prof. Christian Gerloff; deputy coordinator: Dr. Götz Thomalla). The Stroke Quantification Tool (Sonia) has been developed by Fraunhofer MEVIS for the efficient and reliable quantification of stroke MRI data and will allow physicians to integrate the knowledge of leading stroke imaging experts into their individual treatment decisions in real-time. The tool will make routine stroke MRI analysis quicker, more reliable and more effective across knowledge borders and infrastructural boundaries. The incorporation of multiparamentric imaging into acute treatment decisions will lead a step further towards personalized medicine and improved treatment outcomes. The basic idea behind the tool is to allow for a quantitative comparison between the areas of segmented lesions and the segmentations achieved by mirroring the lesions along the medial longitudinal fissure. Note: The stroke quantification tool is not approved as a medical product. 3

4 2. Installation For the installation of the software, the following steps have to be performed. 1. If you have not already received the license file, please contact the coordinator or the deputy coordinator of the WAKE-UP project or contact Fraunhofer MEVIS 2. Download the current version of the software from Note that there might be different versions available (32bit or 64bit). Both versions have exactly the same functions and compute exactly the same results, but the colors of the GUI layout might be different. 3. Double-click the downloaded exe-file and proceed with the installation process (click next). 4. Accept the License agreement I agree so that the software can be installed. 5. Select whether the software should be available for all users of your computer or only for your current user account. 6. Select if you want to install menu shortcuts and/or a desktop icon for starting the software. 7. Select your preferred destination folder where the software should be installed. 8. If starting the software for the first time, you have to define the location of your license file. Fig. 1: Installation process of the Stroke Analysis Tool SONIA. 4

5 3. Data Import The tool is able to import and process DICOM data. For importing the needed FLAIR and DWI data, the following steps have to be performed. Note that also DTI can be used for calculating the ADC maps. For the purpose of readability, this documents used DWI instead of DWI/DTI. 1. Select the root path where subfolders correspond to single cases. In the following example, E:\wake-up-data\ImageData is the root path which stores three subfolders corresponding to three different patient data sets: Fig. 2: Example folder where three patient data sets are stored in subfolders. If your data is not organized this way, you have to disable the Automatic case detection in the settings and directly select the folder of the case which you want to import. For disabling the automatic detection, please refer to the chapter Preferences in this manual. 2. Select the case number which you want to import and process. This is not needed if you have disabled the Automatic case detection. The counting of the number of cases starts with zero. In the example above, case number 0 would correspond to the image data stored in v00, case number 1 corresponds to v00 and case number 2 corresponds to the last one v If you know the series description of the FLAIR and DWI (or DTI) stored in your DICOM data, then please add them (or just a substring of them) into the two text boxes: FLAIR series desc. DWI / DTI series desc. As a consequence, the import process will take less time and the list of imported data sets might be decreased if there are also other sequences available for the case like perfusion, CT, and so on. If you do not know the description, please let the boxes empty. 5

6 Fig. 3: If there is more than one sequence available which fits to the series description, you have to select the correct DWI and FLAIR data in the list below the displayed data. 4. Press the Import button and wait until the data has been imported. If you load the case a second time, the import process will use the already imported cache so that you have to wait only a very short time. 5. Select the FLAIR and the DWI (or DTI) data sets in the lists below the displayed data. 6. If you have made a mistake (like entering a wrong series description) you can re-import the data from scratch by pressing the button (Re-Import). 7. Go ahead to the next step by pressing the yellow arrow at the bottom. 6

7 4. Registration A rigid registration with NGF similarity measure is used for the registration of the FLAIR and DWI data. For the registration process, please perform the following steps 1. Press the button Register. Usually, you have to wait only a few seconds. 2. Verify the registration quality by unchecking and checking the box Registration Result. 3. If you are not satisfied with the result, you might either use the original, non-registered images (just leave the box Registration result unchecked or manually register the images as described in the box Assistance : Left mouse: move overlay Left mouse + shift: rotate overlay Right mouse: reference lookup table Right mouse + shift: overlay lookup table Left mouse + ctrl: navigation You can also reset you changes by clicking the button Reset 4. If your images are in totally different world coordinates, you might pre-align them by pressing the button Pre-align before you press the button Register 5. In case of using DTI data in mosaic format, it can happen the slices are ordered in the wrong way with respect to the z-coordinated. In this case you have to enable the checkbox Flip z-axis. 6. Go ahead to the next step by pressing the yellow arrow at the bottom Fig. 4: A good registration ensures reliable and precise quantification results. 7

8 5. Diffusion Parameters If having DWI data, the diffusion images are stored at different time points in the data set. Usually, the time points are automatically detected. If the detection fails, you can manually adjust them: 1. B0 image: select the time point of the B0 image 2. Bx image: select the time point of the diffusion weighted image with a b-value of x. For example, if x=1000, then you have to specify the time point of the B1000 image. 3. x (b-value): select the correct b-value. Usually, b=1000. Note: the b-value cannot be detected automatically for all scanners, sequences and available versions. Thus, you have to check the value by yourself in all cases. Fig. 5: From the B0 image (left) and the B1000 image (right), the ADC map is calculated. 8

9 6. Brain Segmentation If having selected the correct diffusion parameters, the brain can be segmented by a thresholdbased technique. The larger the threshold, the more skull is stripped from the brain. However, if the threshold is chosen too large, then holes will appear within the brain. After having selected an appropriate threshold, remaining noise/skull can be removed manually: 1. Move the mouse cursor close to the area which should be removed. 2. Ensure that the orange circle does not cover pixels of the brain or skull. That means, the cursor must be somewhere in the background. 3. Keep the left mouse button pressed and move the mouse to erase the remaining noise/skull. 4. Release the mouse button. 5. Repeat the process until you are satisfied with the results. 6. Note: if you have removed too many voxels, you can make them visible again: a. Move the mouse cursor to the area which should be removed. b. Ensure that the orange circle covers completely pixels of the brain/skull. That means, the cursor must be somewhere inside the visible brain or skull. c. Keep the left mouse button pressed and move the mouse to make the area visible. d. Release the mouse button. e. Repeat the process until you are satisfied with the results. 7. If you are not satisfied with the manual segmentation at all, you can press the button Clear correction so that all manual corrections are discarded. 8. Go ahead to the next step by pressing the yellow arrow at the bottom. Fig. 6: A threshold-based technique removes the skull and noise. If there are remaining parts, they can be removed manually as demonstrated here. 9

10 7. Quantification The quantification consists out of two main steps: first, the definition of the mid-sagittal plane, and second, the segmentation of lesions and their automatic mirroring. For the segmentation, all pixels within a region of interest (ROI) are segmented that have an ADC value of at most 620. In addition, slices below and above the ROI are also considered. The number of influencing slices and further parameters can be adjusted (-> Settings). Alternatively, all pixel values within ROIs can be quantified. In detail, the following steps have to be done: 1. Press the button Define 2. If the lesion is within both hemispheres, enable the checkbox Lesion on both sides. Otherwise, disable it. 3. Define three point lying within the mid-sagittal plane. For that purpose, two points within one slice and another point with larger distance to both previously defined point might lead to a good initial mid-sagittal plane. Points can easily be set by a left mouse click in one of the six shown 2D viewers. 4. The plane can be rotated by: a. Move the cursor to the outer ending of the yellow plane (as shown in the screenshot below) so that the cursor changes its appearance ( ) b. Keep the left mouse button pressed c. Move the mouse to rotate the plane 5. The plane can be moved by: a. Move the cursor to the center of the yellow plane so that the cursor changes its appearance ( ) b. Keep the left mouse button pressed c. Move the mouse to move the plane 6. Decide if you want to segment lesions or if you want to quantify all pixel values within ROIs i) Lesion segmentation: a. Press the button Segment b. Choose your favored ROI tool (standard: ellipse) c. Segment the lesion as follows: i. Move the cursor to the lesion ii. Keep the left mouse button pressed iii. Move the mouse to delineate the lesion and release the mouse button iv. Note that you can draw several additional ROIs if needed d. Correct the lesion segmentation if necessary: i. Keep shift-key on keyboard pressed and proceed with the correction process as described previously (-> Brain Segmentation) ii. You can also adjust further parameters used for the segmentation process (-> Settings) ii) Simple ROI quantification: a. Press the button Measure b. Proceed as described before 10

11 7. Indicate further information on the DWI and FLAIR lesions by selecting appropriate values from the selection lists and by adding further comments to the text field. 8. Press the button Update Results 9. Press the button Save Results where you can store the quantification results as pdf document, csv file or just copy the results to the clipboard. In addition you can export the images using your favored file format (Nifti, NRRD, Analyze, DICOM, png, jpg, txt) 10. Go ahead to the next case by pressing the grey arrow at the bottom. Fig. 7: The quantification consists out of two interactive steps: the definition of the mid-sagittal plane by three markers and the delineation of the lesions by a region of interest (ROI). Functionality in 2D viewers: - Zoom in 2D viewer (two alternatives): o Ctrl+Shift and hold center mouse button pressed until desired zoom factor is achieved o + on num-block - Unzoom (two alternatives): o Ctrl+Shift and press center mouse button o 5 on numblock - Case information: press a several times for adding /removing additional information to the viewer - Information on data: press i for further information - Screen splitting: press number from 1 to 9 (not on num block) to show several slices simultaneously - Windowing: press right mouse button and move mouse 11

12 8. Preferences Note that case-specific settings like selected data sets, time points and thresholds are automatically stored for each case separately. Go to Edit / Preferences to change the general preferences. DICOM import - No automatic case detection: see data import (page 4) Registration - You can define the type of used registration algorithm and the type of similarity measure Segmentation - ADC Stroke (Upper Threshold): used for the lesion segmentation: all pixel values within a drawn ROI are segmented if their ADC value is lower than this threshold - Depth of influence (ROI): defines the number of slices which are considered above and below the current slice where the ROI is drawn. For example. If the value is 2, then two slice above and two slices below are considered. On those slices, the drawn ROI is copied and the pixels are segmented accordingly. - Size of lesion segmentation: the borders of the lesion segmentation can be widened by increasing this value. Visualization Check one of the following checkboxes to visualize the appropriate segmentation. Furthermore, adjust the opacity if desired: - Brain segmentation opacity: opacity of the brain segmentation - CSF segmentation opacity: opacity of the corticospinal fluid segmentation. Note that for the CSF segmentation, all ADC pixels are used having a value of at least Stroke opacity: opacity of the segmented stroke lesion - Mirrored stroke opacity: opacity of the mirrored segmented stroke lesion Tags used in report You can defined three DICOM tags and their description which are copied to the final report (pdf, csv or clipboard). Save - Settings file: the location of the file cannot be changed and is displayed only for information purposed - Save: press save to store your modifications - Reset settings: press the button to restore the default settings 12