Hi Tabinda, how to set D depends on the tissue you want to simulate. You can use values from literature, as I did in the Fiberfox MRM publication, or you can use a high-resolution-low-noise in-vivo dataset and measure the ADC, which approximates D. The diffusivity parameters of the individual compartment models (e.g. ISO-D or Axial-Tensor-D) don't have to be equal.
Peter -----Ursprüngliche Nachricht----- Von: Tabinda Sarwar [mailto:[email protected]] Gesendet: Montag, 4. September 2017 02:18 An: Neher, Peter <[email protected]> Cc: [email protected] Betreff: Re: [mitk-users] Modeling multiple fibers in a voxel Dear Peter, Thank you so much for a detailed reply. I have another question. In the compartment model, does the diffusivity parameter 'D' of isotropic compartment should always have to be equal to the axial diffusivity parameters of the zeppelin compartment? As there might be many combinations to simulate the artificial signal but how to know or compute the optimal diffusivity parameters? Thanks and Regards, 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/Diffusi > onImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636 > ac77b8754a707b73f87d21b36882c8bb5$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/Diffusi > onImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636 > ac77b8754a707b73f87d21b36882c8bb5$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
