Hi Matt, 1. how do I access those slices?
To access / extract normally oriented slices MITK provides you the mitkExtractImageFilter. By setting the slice dimension you can tell the filter to extract transversal/coronal/sagittal slices. If you need an example of how to use this filter you can look into the mitkSegTool2D at line 180 -190. If you want to write the processed slice back into your image volume you should use the mitkOverwriteImageFilter, which is used similar to the ExtractImageFilter. Regarding the outlining: What exactly do you want to do? E.g. you could extract single contours out of slices or you could create a complete 3D surface out of your segmentation which is displayed as a 2D contour in the 2D windows and hence outlines your segmentation. Another option is to tell MITK that is should outline your segmentation. In this case you do not have filled contours but just the edges of them displayed in the 2D windows. 2. I am not sure if I understood exactly what you want to do, so please correct me if I got in the wrong direction. Basically you will have 2 objects in the datamanager: your original volume and the thresholded version, i.e. your segmentation. If you want to cut off certain areas of your segmentation of course you could create a new image and put it into the datamanager either. But you can also just delete the appropriate pixel values in your segmentation. The last version should be more efficient, if you don`t need the deleted image information in a later step. Why do you want to update the geometry manually? Normally you don`t have to do that. How exactly do you edit your image? I hope this helps you. Best regards Andreas -----Ursprüngliche Nachricht----- Von: Clarkson, Matt [mailto:[email protected]] Gesendet: Dienstag, 19. Juli 2011 16:35 An: [email protected] Betreff: [mitk-users] Question on thresholding and outlining a 2D slice Hi there, please can I have thoughts on how best to do the following task: Imagine I have loaded a volume, and I'm going to step through a sequence of buttons/sliders that threshold an image, then apply erosions, dilations, a few other ITK filters, and we need to allow manual editing. 1. The first thing is to select thresholds, and an axial slice, below which the image is always thresholded. To keep things snappy, I don't want to be applying thresholds to a 3D image. So, if my orthogonal view planes show 3 slices (axial, coronal, sagittal), how do I access those slices, so I can threshold just them slices, and overlay the outline of the thresholded volume ontop of those same slices? 2. I also need to apply an "Axial cutoff", so I need to select an axial slice, below which the image is thresholded to zero regardless of the minimum and maximum limits set on the slider. THis is so that you can remove the neck easily on an MR image. For this I would need to compute if a voxel had a voxel index below/above the chosen slice, so if in step 1, I have access to the 2D slice I only need a 2D filter, but where would I put this stuff? Do I create 3 new data objects in the DataManager, and update their geometry manually, keeping them in sync with the current slice selection, and let the usual pipelines render them? Or is there a better way? (i hope this makes sense). Once the threshold and axial cutoff slice is chosen, the rest of the application runs on the 3D image, so this is fairly straight-forward in MITK terms, as we simply do image processing in ITK. Thanks Matt ------------------------------------------------------------------------------ Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users ------------------------------------------------------------------------------ 10 Tips for Better Web Security Learn 10 ways to better secure your business today. Topics covered include: Web security, SSL, hacker attacks & Denial of Service (DoS), private keys, security Microsoft Exchange, secure Instant Messaging, and much more. http://www.accelacomm.com/jaw/sfnl/114/51426210/ _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
