Using the Face Masking Pipeline

Transcription

1 1 Using the Face Masking Pipeline We have now made available a Face Masking Pipeline to mask DICOMs to prevent possible patient identification from reconstructed structural images. The pipeline uses a face-masking tool called mask_face developed by the people at NRG Washington University in St. Louis ( Currently we have the pipeline set up such that it does not delete your original DICOMS, but only uploads a second set of defaced DICOMs along with the originals, which you can use if needed. Pipelines are a feature of XNAT that run automatically in the background at the press of a button and can be run on any data that is present in XNAT. The processing takes place on a dedicated cluster in our backend and will not bog up your workstation s resources. You will receive an notification once the processing completes. To start the pipeline: First, make sure the pipeline is enabled for your project. A project owner (usually the PI of the study) can confirm this by going to the Pipelines tab after opening the project. The project owner must enable the pipeline for the project before any members are able to use it. Enable the pipeline by clicking on Add More Pipelines in the Pipelines tab, and then Add besides FaceMasking.xml. Check with the xnat administrator if it is unavailable to you. After logging in, open an MR session in XNAT, and select the sidebar option Processing -> Build.

2 2 This will open a new pop-up window that will display the pipeline options that you have. You can select Face Masking and click Submit. (Continued on next page ->)

3 3 Next, you will see a window that will pre-populate information about the scan. These are the default options and can be changed by you, if needed. Each of the following options that are available for you to change are described below: use_bet - Brain extraction. Set to 1 to generate an exclusion brain mask, 0 to skip this step. Default is 0. mask_ears - 1 for masking ears along with the face. 0 for masking face only. invasiveness - Invasiveness coefficient. Decrease/increase between 0.5 and 1.5 to control the degree of masking and depth of voxel alteration. Default is 1.0. threshold - Background-object intensity threshold. Set to -1 for automatic threshold. ref - Reference scan. Will be registered to atlas, and all other scans registered to the reference. All ROI's are based on reference scan. Select a scan from here as reference only if you are selecting more than one scan to mask. use_manual_roi - Tells the pipeline whether to use (1) or not use (0) manual ROIs. rois - Manual ROI(s) to mask in the reference space. Format: x0,y0,z0-x1,y1,z1. Use "_" delimiter for multiple ROI(s). Cuboid ROI is defined by the outer vertex P0=x0,y0,z0, "above" the surface, and vertex P1, diagonal from P0, "below" the surface. The outer vertex must precede the inner one in a ROI definition.

4 4 dirs - Comma-separated direction(s) for the manual ROI(s), one direction per ROI. 0 - left/right, 1 - top/bottom, 2 - near/far. You may leave all of the above as is, and the defaults will be enforced. Check-box the structural sequences (scan ids) that you d like the pipeline to deface. When selecting more than one scan you will need to choose one of the selected scans as reference: When selecting only one scan to mask, do not select a reference scan. Selecting scans incorrectly will result in your pipeline failing.

5 5 As shown in the image above, the scan-ids correspond to the sequences in the MR session itself. Use this to select the structural scans (STRUC). Hitting Submit should give you a confirmation message like this. The job is now submitted and if you refresh the MR session page, you will be able to see a status bar giving you information about the processing. It may be queued for a while depending on how many jobs are submitted to the cluster at that time.

6 6 When it starts executing it will then update to Running and will give you the percentage of completion (below at ~50%). This is an approximate measure. You do not need to keep track of the status of the processing. Once the processing completes, you will receive an notification, and the same in case of a failure to complete. Please refer to the xnat admin for more details in case of a failure. Receiving the completion notification means, that you are now able to view/download the results. Hovering over the scan file information will show you that the DICOM_DEFACED and DEFACE_QC files have now been uploaded. They will be present along side the DICOM files.

7 7 You may have a look at the files from the Manage Files menu button. This brings up a file manager that will let you browse the files that have been generated by the pipeline and view/ download them. The files generated will lie at scan level and be available in two folders, DICOM_DEFACED, which contains the original DICOMS with the face pixels masked, and DEFACE_QC, which contains two image files showing the reconstructed DICOMS and their masked faces/ears. Clicking on the png files will open them in the browser. To download, you can uncheck all boxes and then just select the DICOM_DEFACED folder and/or DEFACE_QC folder and click on Download.

8 NYSPI MRI Unit These files can also be downloaded with the DICOMs when the entire scan session is downloaded (optional). Results: DICOM_DEFACED: complete set of original full resolution DICOMs with face and/or ear pixels removed. DEFACE_QC: Two QC images to view the results of the face masking. a)study*_normfilter.png- sample of masked slices from the DICOMs: 8

9 9 b)study*_normfilter_surf.png - a reconstructed sample of the complete face-masked structural volume. for more information refer to: Author: Aniqa Arif