Commit ef2b0581 authored by Menzel, Miriam's avatar Menzel, Miriam

add troubleshooting statement

parent 2ca65476
......@@ -67,6 +67,9 @@ By evaluating the SLI profiles of each image pixel, *SLIX* generates different p
With [`SLIXLineplotParameterGenerator`](#evaluation-of-sli-profiles), it is possible to evaluate individual SLI profiles and compute characteristics such as the number of peaks, their positions, and in-plane fiber direction angles. For a given SLI image stack, [`SLIXParameterGenerator`](#generation-of-parameter-maps) computes the desired parameter maps for all image pixels.
## Installation of SLIX
Note: The current version of SLIX can only be executed under macOS or Linux as operating system because of dependencies. If you want to use SLIX under Windows, please use the [Windows Subsystem for Linux](https://ubuntu.com/wsl). Support for Windows is planned for the future.
##### How to clone SLIX (for further work)
```
git clone git@github.com:3d-pli/SLIX.git
......@@ -240,7 +243,9 @@ SLIXParameterGenerator -i ./Vervet1818_s0512_60um_SLI_090_Stack_1day.nii -o .
`_peakdistance.tiff` shows the distance between two prominent peaks for each image pixel. If an SLI profile contains only one peak, the distance is zero. In regions with crossing nerve fibers, the distance is not defined and the image pixels are set to `-1`. The peak distance is a measure for the out-of-plane angle of the fibers: A peak distance of about 180° implies that the region contains in-plane fibers; the more the fibers point out of the section plane, the smaller the peak distance becomes. For fibers with an inclination angle of about 70° and above, a single broad peak is expected.
##### Direction Angles
The in-plane direction angles are only computed if the SLI profile has one, two, four, or six prominent peaks with a pair-wise distance of (180 +/- 35)°. Otherwise, the image pixel is set to `-1`. The direction angle is computed from the mid position of one peak pair, or (in case of only one peak) from the position of the peak itself. All direction angles are in degrees (with 0° being along the positive x axis, and 90° along the positive y-axis).
The in-plane direction angles are only computed if the SLI profile has one, two, four, or six prominent peaks with a pair-wise distance of (180 +/- 35)°. Otherwise, the image pixel is set to `-1`. The direction angle is computed from the mid position of one peak pair, or (in case of only one peak) from the position of the peak itself. All direction angles are in degrees (with 0° being along the positive x axis, and 90° along the positive y-axis).
In case of three or five prominent peaks, the peak pairs cannot be safely assigned and are therefore not evaluated. SLI profiles with three peaks could also be caused e.g. by strongly inclined crossing fibers, where a reliable determination of the in-plane fiber directions is not possible. If an SLI profile contains three prominent peaks, it might also be the case that the forth peak lies below the prominence threshold because the signal is not very clear. To account for missing peaks, the user has the possibility to decrease the prominence threshold by setting another value with `--prominence_threshold`. However, this should be done with caution, as this also causes non-significant peaks that are generated by noise or other artifacts to be considered for evaluation and might yield wrong fiber direction angles. Therefore, we strongly recommend to read the derivation in [Menzel et al. (2020)](https://arxiv.org/abs/2008.01037), Appx. A, before adjusting the threshold.
<img src="https://jugit.fz-juelich.de/j.reuter/slix/-/raw/assets/dir_1.jpg" width="327">
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