This document contains step by step instructions as a memory aid for those preparing cases.

Transcription

1 Case harvesting document This document contains step by step instructions as a memory aid for those preparing cases. Everyone else just needs to remember to bring their laptop and encrypted hard drive to the session, and refer to page 10 if you need a reminder of how to transfer cases onto your external hard drive. Contents P2-3 Osirix anonymisation protocol (Mac users) P4 Getting rid of demographic details and red dot marks from images! Shutter tool method! Pixel shift method P5-9 DICOM cleaner (necessary for PC users, optional for Mac users) P10 Exporting cases to share with your year group P11-12 Attaching jpeg answers P13 Optional extras! Re-orientating and annotating images! Indexing your personal collection Prepared by H Matthews & S Shamshuddin for North West School of Radiology.

2 Anonymising using OsiriX Anonymisation protocol (1) Launch OsiriX. Ensure you have selected the appropriate database on your EHD in the Sources pane on the left side (eg 01 Rapid reporting). Click Import icon on toolbar, navigate to your cases (eg folder within EHD or CD supplied by PACS manager). Single click on the folder to select, then click Open button. Select copy files button. Imported files will now appear in your database window. Click one case to highlight, then click Anonymise icon in toolbar (red arrow above) (older versions, Menubar>file>anonymize) Choose the appropriate anonymisation protocol from the dropdown list (red arrow below). Change the details in the highlighted fields for your case (eg RR01.02 for second case in the first set of rapids you create, or LC01.01 for the first of a set of long cases). Note that Patient ID, Patient name and StudyInstanceUID should be the same within any one case.

3 Anonymising using OsiriX Anonymisation protocol (2) Click Replace button. At this message (above) click OK (it seems counterintuitive, but you want to delete the unanonymised case and replace it with the renamed version...). The renamed case will then appear in the database window. Finally, click the metadata icon and scroll through the list to make sure that no patient identifiable data remains. If you do find something has slipped through, make a note of the field name and number and add this to your anonymisation protocol. Adding fields to anonymisation protocol Highlight case in database window, click anonymise icon. At the bottom of the list click the grey arrow to the right of select a DICOM tag (red arrow) Choose either sort by name of sort by value, and scroll down the list until you find the field name /number you noted earlier. Click the grey +. (purple arrow) Repeat for any more fields you need to add if you noted more than one Click Save, give your new anonymisation protocol a name, then click Save. Your new protocol will now appear in dropdown menu and can be used to re-anonymise the case where patient details had slipped through, and for future cases too.

4 Getting rid of demographic data and red dot markers using Osirix Shutter tool method for single or multiple images (eg rapids cases, CT series) Open the image or series you wish to change. Select rectangle tool from dropdown menu in toolbar and place over the area you wish to keep (place cursor at one corner of desired position, then hold left mouse button and move cursor to opposite corner of desired position, then release left mouse button) Click shutter tool icon, then hit backspace key to remove rectangle marker. Click DICOM file tool (or Menu bar>file>export>export to DICOM) Choose Image format As displayed in 16-bit BW, select either single image or series as appropriate, and give your new image(s) a name. Then click OK. Your altered images will now be listed as a new DICOM series. Finally, return to the database window, highlight the thumbnail of the original, unanonymised image/series and hit backspace to delete it, leaving only the new altered/anonymised DICOM image/series. Pixel shift method for single or multiple images Open the image or series* you wish to change. Select rectangle tool from dropdown menu in toolbar and place over the area you wish to remove. Multiple rectangles may be placed to remove several areas of unwanted information. * For image series, there is an additional step here; go to Menu bar>roi>propagate selected ROI, check entire series and duplicate ROIs, click OK. Then click Set pixels icon. (or Menu bar>roi>set pixel values to...) Check ROIs with same name..., Inside ROIs. Click OK. Hit backspace key to remove pink/green box. Click DICOM file tool (or Menu bar>file>export>export to DICOM) As with Shutter method above, choose Image format As displayed in 16-bit BW, select either single image or * series as appropriate, and give your new image(s) a name. Then click OK. Finally, return to the database window, highlight the thumbnail of the original, unanonymised image/series and hit backspace to delete it, leaving only the new altered/anonymised DICOM file.

5 Using DICOM cleaner (1) Import folders onto your encrypted external drive from CD/USB Connect encrypted hard drive (EHD) to USB port, enter your PIN number followed by padlock symbol, wait until light glows constant green. Open EHD to view folders. Insert CD or USB device upon which your PACS manager has put the cases he/she has exported from PACS and open this to view folders. Drag and drop your cases from the CD/USB provided by your PACS manager into the DICOM cleaner Edit folder in your external hard drive, then eject the CD/USB provided by your PACS manager. Launch DICOM cleaner to display window illustrated below. Click Import button Navigate via Volumes > (your EHD s name )> 03 DICOM cleaner > 01 Edit folder Single click on folder containing case(s) to be anonymised Click Choose button You will now see the case folder(s) displayed in the original window pane

6 Using DICOM cleaner (2) Click once on a folder in original window pane to highlight Check/uncheck boxes as illustrated above* Replace pt name and pt ID with your unique code-sequential number (First 3 letters of your first name and First 3 letters of your Surname-0001; HILMAT-0001) Click clean button and your renamed case will appear in the right hand Cleaned pane *Old versions of DICOM cleaner may have a 'remove contributing equipment' rather than 'add contributing equipment'. If you are using such a version, please check remove contributing equipment.

7 Using DICOM cleaner (3) Using DICOM cleaner BLACKOUT to remove patient details from images If this step is required, highlight your case in right hand pane and click blackout button. If not, skip to next page. Hold right mouse button to place box over area to be deleted (repeat to draw another if you need 2 areas deleted). Check either use padding or use zero (it doesn t matter which, unless you re fussy about what shade of rectangle you get on the final cleaned images!) Click apply all and save to blackout the marked areas on all images in series Using DICOM cleaner BLACKOUT to remove red dot markers For single images, eg removing a red dot marker from one image in a series, you can use a slight modification of the above technique (use next button to select the image you want to blackout, draw your box(es), click apply then save ).

8 Using DICOM cleaner (4) In right hand pane, highlight case(s) to be exported. If you want to get rid of unwanted series (eg CT dose reports or MR localisers), click the small grey triangle to display subfolders and highlight only those which you wish to retain. Click Export button Navigate via Volumes > (your EHD s name )> 03 DICOM cleaner > single click to highlight 02 cleaned folder, click Choose button Wait for message done exporting to to appear at the bottom of the screen, then close or minimise DICOM cleaner.

9 Using DICOM cleaner (5) Finally, import cleaned cases to Osirix; Launch Osirix, then select the appropriate database on your encrypted hard drive in the sources list (red arrow). Click import (purple arrow) Navigate to EHD>Osirix master folder>dicom cleaner>cleaned folder Select case(s), then click Open button When asked, choose Copy files. Your new, renamed, cleaned case (s) will then appear in the Osirix database window ready for your teaching session. Housekeeping for your EHD Now that you have cleaned your cases, go back into the DICOM cleaner Edit folder on your EHD and delete your original, incompletely anonymised cases. It is also recommended to empty the DICOM cleaner Cleaned folder at this stage, to avoid re-importing the same cases next time you use DICOM cleaner.

10 Sharing cases with your year group Create a suitably labelled folder on your encrypted hard drive eg SHARE (open EHD, right click, new folder). Create Sub-folders within this: 01 Rapid Reporting, 02 Long Cases and 03 Interesting Cases (this is to enable smooth functionality for the PC users in the group) Open OsiriX Select the appropriate database source (eg Rapid Reporting DB) Highlight the cases you wish to share with the group (eg 30 rapid cases) Click File (menu bar) > Export > Export to DICOM file(s) Navigate to the folder you created earlier ( eg 01 Rapid Reporting) under the SHARE in your EHD Select Flat folder tree and Decompress all DICOM files. Click Choose button. Export Long Cases and Interesting Cases as above to respective folders in the EHD You can now transfer/copy paste this SHARE folder to the encrypted hard drives of other group members very simply by opening both your external hard drives on one laptop, then just drag and drop the share folder to copy it onto your colleague s external hard drive. Please do not use networking or unencrypted USB drives to copy cases.

11 Attaching jpeg answers For each long case, and for each set of rapids, you should prepare an answer sheet, and attach this as a jpeg file with the image sets on the NWSOR library EHD. First create a folder on your encrypted hard drive to save these to eg Answers (open EHD, right click, new folder) Create your specimen answer as a word/pages document, then use the screenshot function to convert this to image format (keyboard shortcut; hold command and shift, and press 4 simultaneously, use mouse/trackpad to select area of screen to be captured as image, same technique as placing rectangular ROI in Osirix). The screenshot image will save to desktop as Screenshot dd.mm.yy. at hh:mm, from where you can rename it to something more appropriate (eg Answers RR ) Launch Osirix and in database window highlight the case you wish to add the jpeg image to. In the bottom pane click once on the thumbnail of the last series in your case to ensure the answer gets put at the end, rather than in the middle! Click Plugins (menubar) > Database > JPEG to DICOM > Navigate to the appropriate jpeg answer sheet > click Open. The specimen answer is now attached as a DICOM image with the image series relating to that case.

12 Appendix 1 Sample specimen answer (courtesy of RCR website)

13 Appendix 2 Optional extras for Mac users Reorientating and annotating images Use the mouse button functions to mark arrow, rotate, resize or reposition images as required. Then click DICOM file tool icon (or Menu>File>>Export>Export to DICOM file...) Check buttons by Current image and As displayed in 8 bit with ROIs. Give the new image a name and click OK. Labelling your personal collection If you wish to index your personal collection in Osirix, you can enter details into either the Comments 2,3 and 4 fields (click in bottom left corner of cell on database page and type), or into searchable DICOM fields eg Institution, Performing physician and Referring Physician fields (using the anonymisation protocol tool) The Osirix usergroup labelling conventions are;! Comments is not used as it appears on image thumbnails! Comments 2 = diagnosis and key words (eg facial fracture, le fort 1)! Comments 3 = age and gender, brief history (eg 23M, assault)! Comments 4 = RCR modules Please be aware that Comments 2, 3 and 4 are not DICOM fields therefore are inaccessible unless using OsiriX or backed up as separate Excel file (For more information see video tutorial 6 on UK Osirix usergroup website). For this reason, some users prefer to index their cases using the searchable DICOM fields (right click on column titles in database window to see full list and/or select which fields you wish to display).