It works great! Thank you!
Cheers,
Patricio
2017-01-23 11:02 GMT-03:00 Neher, Peter <[email protected]>:
> No need to build it yourself. The binary is fine. The current source just
> has more features.
>
>
> The issue is the fiber radius. If you leave it at 0 (default value), then
> the fiber radius is estimated based on the number of fibers in the
> "fullest" voxel. If you set it manually, in this case 3µm, you won't see
> anything if there are not enough fibers in the voxel. So, either you
> generate much more fibers to increase the fiber density, or you set the
> fiber radius to 0 for automatic estimation. This should fix your issue. Let
> me know if it works!
>
>
> Peter
>
>
>
> ________________________________
> Von: Patricio Donnelly Kehoe <[email protected]>
> Gesendet: Montag, 23. Januar 2017 14:50
> An: Neher, Peter
> Cc: [email protected]
> Betreff: Re: [mitk-users] [Fiberfox] Low range of values in generated
> Nifti using Fiberfox
>
> Hello Peter, I'm using the binaries in Ubuntu 14.04. The acquisition
> parameters are the default ones:
>
> Signal Scale: 100
> TE: 100
> Line Readout Time: 0.84
> Time homogeneity relaxation: 50
> Fiber Radious: 3
>
> Values range are very limited (only one value between fiber voxels and
> nonfiber voxels) in B0 and non B0 images. For each the ranges are:
>
> B0
> Nonfiber voxel: 189
> Fiber Voxel: 190
>
> Non B0
> Nonfiber voxel: 70
> Fiber Voxel: 71
>
> Do I have to compile from source?
>
> Thanks,
> Patricio
>
>
> 2017-01-23 6:21 GMT-03:00 Neher, Peter <[email protected]<mailto:
> [email protected]>>:
> Hi Patricio,
>
> you are talking about b0 intensities, right? 70 seems pretty low in
> general. What is your signal scale parameter? Maybe you set that to a value
> one order of magnitude higher.
>
> Your model parameters seem fine. In general, the shorter the echo time,
> the lower the contrast because there is not enough time for the signal to
> decay. How long is your echo time?
>
> Are you using the MITK Diffusion installer or did you build it yourself?
>
> Cheers,
> Peter
>
> Von: Patricio Donnelly Kehoe [mailto:[email protected]<mailto:
> [email protected]>]
> Gesendet: Freitag, 20. Januar 2017 20:48
> An: [email protected]<mailto:mitk-users@lists.
> sourceforge.net>
> Betreff: [mitk-users] [Fiberfox] Low range of values in generated Nifti
> using Fiberfox
>
> Hello, I'm using Fiberfox to generate very simple fiber geometries and I
> keep getting Nifti files with very low range of intensities between fiber
> and non fiber voxels. I want to know if I'm doing anything wrong or if this
> behavior is expected.
> I have been playing around with the model values, but I can't get a big
> range of intensity values. For example, the difference between fiber and
> non fiber voxels is only one unit of intensity values (71 and 70).
> Maybe I'm configuring badly the parameters in the model configuration
> between intra-axonal, extra-axonal and extra-axonal compartments.
> Intra-axonal values are:
> T2-relaxation: 110 ; FA: 0.97
> Inter-axonal values:
> T2-relaxation: 110 ; FA: 0.97
> Extra-axonal values (Ball-model):
> T2-relaxation: 80
> If needed I can provide more information.
> Thanks,
>
> --
> Bioengineer Patricio Donnelly Kehoe
> PhD Student at CIFASIS - CONICET
> Multimedia Signal Processing Group - Neuroimage Division
> http://www.cifasis-conicet.gov.ar/
> Contact Number: +5493412164799
>
>
>
>
> --
> Bioing. Patricio Donnelly Kehoe
> PhD Student at CIFASIS - CONICET
> Multimedia Signal Processing Group - Neuroimage Division
> http://www.cifasis-conicet.gov.ar/
> Contact Number: +5493412164799
>
>
--
Bioing. Patricio Donnelly Kehoe
PhD Student at CIFASIS - CONICET
Multimedia Signal Processing Group - Neuroimage Division
http://www.cifasis-conicet.gov.ar/
Contact Number: +5493412164799
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