Hi Ellankavi, generally it is best to keep the discussion on the list, so others can weigh in.
We do have the documentation to help users do a simulation (either hit F1 in the application or http://docs.mitk.org/nightly/org_mitk_views_fiberfoxview.html ), but AFAIK we do not have a comprehensive tutorial. We are currently working on some general video tutorials on setting up MITK (no ETA, sorry), but those are not going to cover specific views like fiberfox. If you are willing to create one (video or text), we would be happy to point people to it. Best, Caspar Von: Ramasamy, Ellankavi [mailto:ellankavi.ramas...@ipa.fraunhofer.de] Gesendet: Dienstag, 13. September 2016 10:23 An: Goch, Caspar Jonas Betreff: AW: Fiberfox tissue mask Hello Caspar, Thanks for the information.. I had found through trial-and-error that I can use the 'Fiber Processing' module to create the binary mask for the fibre bundle and use morphological closing in basic image processing module to create a full mask. Is there already a tutorial to simulate DT-MRI images? I wasn't able to find one online. Maybe I can help you make one? Thanks, Ellankavi Von: Goch, Caspar Jonas [mailto:c.g...@dkfz-heidelberg.de] Gesendet: 12 September 2016 14:55 An: Ramasamy, Ellankavi; 'mitk-users@lists.sourceforge.net' Betreff: AW: Fiberfox tissue mask Hi Ellankavi, assuming you are using the 2014.10.02 release, you should be able to add a tissue mask just by CTRL-clicking on it and the fiber bundle. When both are selected the "Tissue Mask" label should change to the name of the image being used as a tissue mask. Please note, that it should be a binary image mask (they are denoted by a special icon in the datamanager, where an image has a 5 by 5 grey value matrix icon, the binary masks icon contains red voxels symbolizing a segmentation). If your tissue mask is recognized as a regular image you can force it to be treated as a segmentation by selecting it in the Properties View and checking the "binary" property. Alternatively you can use the thresholding option of the Basicimageprocessing view. Best, Caspar Von: Ramasamy, Ellankavi [mailto:ellankavi.ramas...@ipa.fraunhofer.de] Gesendet: Donnerstag, 8. September 2016 12:28 An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Betreff: [mitk-users] Fiberfox tissue mask Hello, I'm new to MITK and interested in creating a DW-MRI phantom using the Fiberfox module. I'm able to create the fiber bundle but I'm unable to add a tissue mask to the data. How can I add a tissue mask to the fiber bundle? Thanks Warm regards, Ellankavi
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