Hi Peter! Just for my clarification I wanted to ask that if there is no fiber density at a particular location or voxel, then there is only one compartment which is isotropic. So will the volume fraction 'f' in the attached equation be used (i.e. the signal=f*exp(b*D1) or there is no need of volume fraction 'f' (i.e. the signal=exp(b*D1)? http://mitk-users.1123740.n5.nabble.com/file/t737/image714.png
Tabinda On Fri, Sep 1, 2017 at 9:47 PM, Neher, Peter <[email protected]> wrote: > Dear Tabinda, > > > welcome on the MITK mailing list. > > > 1. The integral is approximated by sampling the fibers equidistantly (1/10 * > min. voxel size) and summing the signals at these positions: > > https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$999 > > > 2. Not sure what you mean by this. The signal is calculated as described in > the formula you posted in your first question. There is no average but a sum > of the signals from the different sources: > https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$1036 > > 3. Without explicitly setting volume fraction images, the volume fraction of > the anisotropic compartment corresponds to the fiber density at this > location. If no fiber is present, the fiber density is zero and therefore > there is no anisotropic compartment. > > I hope this helps. If you have more questions, don't hesitate to ask. > > Peter > > _____________________________________ > Von: tabinda <[email protected] > Gesendet: Freitag, 1. September 2017 11:50 > An: [email protected] > Betreff: [mitk-users] Modeling multiple fibers in a voxel > > > Hi! > > I am Tabinda. I have been using the Fibercup phantom simulated using > Mitk-Fiberfox for evauluating different tractography algorithms and now I am > trying to replicated the same Fiberfox simulated phantom. I have three > queries regarding the paper "Fiberfox: Facilitating the Creation of > Realistic White Matter Software Phantoms" > > 1. How to compute the integral given in eq (2) of the paper? (image > attached) > <http://mitk-users.1123740.n5.nabble.com/file/t737/image714.png>; > > 2. I have read in other papers that weighted average is used to compute the > multiple fibers in a voxel but this interpretation is new for me. I couldn't > find the source code on the MITK Phabricator > (https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/FiberTracking/Fiberfox/). > > 2. If I use weighted average for modeling multiple fibers in a voxel, the > amplitude of fiber orientation estimated for parallel fibers doesn't add up > like Fiberfox simulated fibercup (image attached) > <http://mitk-users.1123740.n5.nabble.com/file/t737/image2.png>; > > How this pattern is modeled in fiberfox? > > 3. In a voxel in which there is no fiber orientation (e.g. gray matter), > what is the value of the anisotropic compartment? Is it zero or one? Or > some specific value is given to the Tensor 'D' in case of isotropic > compartment? > > Help regarding these queries will be highly appreciated. > > Thanks and Regards, > Tabinda > > > > -- > Sent from: http://mitk-users.1123740.n5.nabble.com/ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > mitk-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mitk-users ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
