Dear Tabinda, Fiberfox applies a global scaling factor to the signal that is defined in the GUI. I think the default is 100. This is necessary since the image values are stored as 'short' variables. You can change this factor however you like. Furthermore, the signal scales with the voxel volume, as it is the case in real MR images. In this case by a factor of 3x3x3 = 27, since the image spacing is 3mm. A simulation without relaxation would therefore result in a b=0 signal intensity of 2700. The relaxation reduces this to the roughly 800-850 that you observed.
Peter -----Ursprüngliche Nachricht----- Von: tabinda <tsar...@student.unimelb.edu.au> Gesendet: Freitag, 11. Mai 2018 02:23 An: mitk-users@lists.sourceforge.net Betreff: [mitk-users] Understanding dMRI Simulation using Fiberfox Hi! I am Tabinda. I have been using the Fibercup phantom simulated using Mitk-Fiberfox. According to the ball-zeppelin model for phantom simulation given in "Fiberfox: Facilitating the Creation of Realistic White Matter Software Phantoms" (image attached), the isotropic compartment should not be having high intensity. <http://mitk-users.1123740.n5.nabble.com/file/t737/zbmodel.png> According to the equation, the isotropic compartment is given as fv*exp(b*D1) where fv is the volume fraction for isotropic compartment, b is the b-value and D1 is the isotropic diffusion. Calculating these value results using the parameters provided in the paper gives 0.033 whereas the simulated phantom (B2.nii.gz- region outside the fibers) has the intensities between 800-850. Even after the simulation of k-space (equation attached-fraction of the simulated signal), how come the isotropic compartment ends up with high intensities? <http://mitk-users.1123740.n5.nabble.com/file/t737/kspace.png> Is there something which I am missing? Your timely response will be highly appreciated Thanks, 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
