Thank you Peter. You response has clarified my confusion.
Tabinda
On Fri, May 11, 2018 at 4:31 PM, Neher, Peter <p.ne...@dkfz-heidelberg.de>
wrote:
> 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/
>
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