Hi Miguel, MITK always uses world coordinates for the fiber points. Thus, no transformation is needed and the matrix is set to identity. The bounding box of the fibers is different from the image bounding box since the fibers don't necessarily have to occupy the same volume as the image they were obtained from.
Regarding your second question, the fiber colors are calculated in the FiberbundleX class. The default orientation colorcoding is calculated in DoColorCodingOrientationBased() and a custom color coding, e.g. FA based color coding, is done in the method "SetFAMap" of the FiberBundleX. I hope that helps! Cheers, Peter On 14.10.2014 18:18, Miguel Nunes wrote: > Hello MITK List, > > I am having a interesting problem. I am loading a Track file (trk) and the > respective accompanying MR datasets and segmentations. > > After loading the datasets, all datasets are correctly aligned in the > stdmultiwidget. > > But for my plugin I need to access the transformation between the datasets > and I cannot achieve this. There is always some miss calculations. For > example, if I ask the geometry3D for the bounding box of the dataset, it > gives me different values comparing to when I get these values from the > vtkPolyData inside the mitkFiberBundleX. The two returning BB are not the > same. > > When I check the details of the Fiber dataset, it is only shown an identiy > matrix and the BBox, without any transformation. But the BBoxes of the track > and the MR image are different. So, how does MITK align them? > > Also, I do not understand how the colors of the fibers get rendered. As far > as I have found there is only a > fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_CUSTOM) (and similar) > which leads me nowhere. the render functions of geometry only lead me in > circles... > > Thank you! > > Best regards, > Miguel Nunes > > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://p.sf.net/sfu/Zoho > _______________________________________________ > mitk-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mitk-users -- Dr. sc. hum. Peter F. Neher Division Medical and Biological Informatics Junior Group Medical Image Computing (MIC) German Cancer Research Center (DKFZ) Im Neuenheimer Feld 280 69120 Heidelberg Germany phone: +49 6221 42-3552 fax: +49 6221 42-2345 [email protected] http://www.dkfz.de/de/mbi/people/Peter_Neher.html Confidentiality Note: This message is intended only for the use of the named recipient(s) and may obtain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
