Thank you very much for your help Tabinda
On Mon, Sep 4, 2017 at 3:56 PM, Neher, Peter <p.ne...@dkfz-heidelberg.de> wrote: > 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:tsar...@student.unimelb.edu.au] > Gesendet: Montag, 4. September 2017 02:18 > An: Neher, Peter <p.ne...@dkfz-heidelberg.de> > Cc: mitk-users@lists.sourceforge.net > 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 <p.ne...@dkfz-heidelberg.de> > 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 <tsar...@student.unimelb.edu.au >> Gesendet: Freitag, 1. September 2017 11:50 >> An: mitk-users@lists.sourceforge.net >> 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 >> mitk-users@lists.sourceforge.net >> 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 mitk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mitk-users
