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:[email protected]> 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 ------------------------------------------------------------------------------ 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
