v1.0.0-rc3

Trekker v1.0.0-rc3 now out!

What's Changed

• New feature: track can now save seed indices as a vtk field.
• Bug fix 1: Fixed an issue when stopping rule was ignored when a seed was places on edges.
• Bug fix 2: Fixed an issue with segment surface intersection.
• Bug fix 3: select indexing fixed.
• Bug fix 4: Fixed an issue preventing streamline truncation at max length in some cases.
• Bug fix 5: Fixed MacOS support.
• Bug fix 6: Fixed Windows support.
• Bug fix 7: tran_shi_2015 model no more gets stuck when running.
• Improvement 1: Added stricter pathway rule validation for track and filter.
• Improvement 2: In filter, changed option name --seedTrials to --seed_trials to be consistent with track. Also added --output, -o option for the same reason.
• Improvement 3: Seedless filtering now works independent from online filtering and it works faster.
• Improvement 4: Upgraded to CLI11-v2.4.2
• Improvement 5: Provided stand-alone executables for macOS and Windows.
• Improvement 6: Provided basic test routines.

v1.0.0-rc2

Trekker v1.0.0-rc2 now out!

What's Changed

• Bug fix 1: Fixed a bug which prevented using negative labels for selecting surface ROIs.
• Bug fix 2: Fixed a bug in track2surf that was introduced as a result of the major updates in rc1, which led to the saving of wrong field information for mapped streamlines on surface meshes.
• Improvement 1: Added a new command info, which prints basic information about input files.
• Improvement 2: Added option to flip surface normals when defining pathway rules.
• Improvement 3: Added option to use only the surface boundary when the provided mesh is closed for defining pathway rules.
• Improvement 4: (As a solution to the nibrary issue submitted by Xi Zhu) Added option to use ascii (text) files for defining seed density for fiber tracking with surface-based seeding.
• Improvement 5: Random seeds are now sampled using an approach based on cumulative distribution function instead of rejection sampling.

v1.0.0-rc1

We are excited to announce the first release candidate. Trekker v1.0.0-rc1 includes bug fixes and improvements, particularly in surface handling. See below for a list of major changes.

What's Changed

• Bug fix 1: Fixed a bug in track where streamlines were not stopped as expected when a pathway rule was set. This issue occurred because track allowed stop options unsupported by nibrary. The fix involved providing nibrary with the necessary stopping features during tracking.
• Bug fix 2: (Thanks to John Kruper for spotting this one!) Fixed a bug in track related to the computation of data support in parallel transport tracking. Previously, the contribution from the last part of the probe was reused as the first part's contribution in the next iteration to speed up computation. This fix ensures the data support contribution is computed only once for the first part and reused for other candidate probes. Although this bug has existed since v0.5, it should not significantly affect results with default probe quality (4) and length (0.25 x voxel size). However, it may impact streamlines computed with longer probe lengths and lower quality probes.
• Bug fix 3: Fixed a bug affecting both track and filter, where streamlines were not following the require_end_inside rule. The issue occurred because this rule was commented out during a part of the development in nibrary, and it was forgotten to be restored.
• Improvement 1: Reorganized the code to harmonize the handling of segment-surface interactions.
• Improvement 2: Switched to the double datatype in certain functions to better manage edge cases.

v1.0-beta

We are excited to announce the release of Trekker v1.0 beta, now available for testing!