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/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$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/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp;5880636ac77b8754a707b73f87d21b36882c8bb5$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 <[email protected]
Gesendet: Freitag, 1. September 2017 11:50
An: [email protected]
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
--
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