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Expanded tractography file format support - #3415

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Expanded tractography file format support#3415
Lestropie wants to merge 100 commits into
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trx

Commits on Jun 11, 2026
- Stage 1 Step 1: format-handler back-end framework
  
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- Stage 1 Step 2: move Reader/Writer into formats/tck.{h,cpp}
  
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- Stage 1 Step 3: move tck backend impl to tck.cpp via explicit instantiation
  
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- Stage 1 Step 4: implement Tractogram accessor
  
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- trx: extract generic RAM write-back buffer (WriteBuffer)
  
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- trx: move the .tck RAM write buffer into WriteBuffer
  
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- trx: generalise WriteBuffer for cross-format reuse; reuse it in .tsf
  
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- tckconvert: route generic conversion through the Tractogram framework
  
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- Stage 4: add .vtk legacy PolyData format handler (read+write, ASCII+binary)
  
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- Stage 4: remove bespoke .vtk handling from tckconvert; route via framework
  
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- Stage 5: Create write handler for tractography data in `.vtx format`. Both ASCII and binary data will be supported.
  
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- Stage 5: Create read handler for tractography data in `.vtx` format. Both ASCII and binary data will be supported. Unlike the `.vtk` format read handler, where the content of the `LINES` data block…
  
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- Stage 5: De-duplicate code between the `.vtk` and `.vtx` tractography format handlers, hosting code in `cpp/core/dwi/tractography/formats/vtk_utils.(cpp|h)`.
  
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- Stage 6 step 1: optional Header on format-handler base class
  
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- Stage 6 steps 2-3: interpret .tt format; write tt_parsed.md (out-of-repo)
  
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- Stage 7 step 2: implement DSI Studio .tt read & write handlers
  
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- Stage 7 step 3: buffer .tt track writes; add round-trip/coordinate/negative tests
  
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- Stage 8 step 1: research Unix pipe internals for tractography pipe handler
  
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- Stage 8 step 2: decide pipe transport strategy (raw-binary-stream)
  
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- Stage 9.1: Unix-pipe tractography read & write handlers
  
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- Stage 9.2: pipe error-path tests (broken pipe / premature close)
  
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- Stage 9.3: reject random-access requests against streaming-only handlers
  
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- Stage 10 step 1: expand Streamline / introduce composite sidecar item
  
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- Stage 10 step 2: Shared field-registry context for worker functors
  
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- Stage 10 step 3: tckconvert carries the full TractogramItem sidecar
  
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- Stage 10 step 4: pipe handler carries arbitrary sidecar data
  
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- Stage 11 steps 1-2: tractogram-sidecar CLI argument types
  
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- Stage 11 step 3: adopt tractogram-sidecar argument types on sidecar options
  
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- Stage 11 step 4: parse the path::name tractogram-sidecar reference syntax
  
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- Stage 11 step 5: inject standalone input-sidecar data per streamline
  
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- Stage 11 step 6: export processed sidecar data to standalone files
  
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- Stage 11 step 7: reject .tsf export under a random-access request
  
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- Stage 12 step 1: audit C++ commands that read/write tractography or sidecar data
  
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- Stage 12 step 2: tckresample updates dpv to output vertices
  
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- Stage 12 step 3: tckedit/tcksift embedded streamline-selection dps field
  
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- Stage 12 step 4: tcksift2 opt-in embed weights via append capability
  
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- Stage 12 step 5: tcktransform passes dpv and dps through unchanged
  
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- Stage 12 step 6: connectome2tck carries dps/dpv/weights to sub-tractograms
  
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- Stage 12 step 7: tcksample write-time per-vertex consistency check
  
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- Stage 12 step 8: tckvalidate validates any format + dps/dpv field lengths
  
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Commits on Jun 12, 2026
- Stage 13 (steps 1-2): VTK sidecar field mapping
  
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- Stage 13 (step 3): VTK write handler sidecar support
  
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- Stage 13 (step 4): VTK read handler sidecar support
  
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- Stage 14 step 2: byte-packed TrackVis .trk header struct
  
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- Stage 14 step 3: TrackVis .trk write handler
  
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- Stage 14 step 4: TrackVis .trk read handler
  
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- Stage 14 step 5: stamp COMMAND_STRING into the .trk header
  
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- Stage 14 step 6: .trk capability flags, registration and tests
  
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- Stage 15.1: random-access RAM wrapper for streaming tractography formats
  
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- Stage 15.2: auto-select the RAM wrapper for streaming-only random access
  
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- Fix dangling field-registry reference in Tractogram open()/create()
  
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- TRX (steps 1-2): parse a TRX directory and summarise sidecar data
  
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- TRX (steps 3-5): archive sources and the initial read-only handler
  
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- TRX (steps 6-7): parse the JSON header and load vertex + sidecar data
  
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- TRX (step 8): create_tempdir + signal-handler cleanup for compressed archives
  
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- TRX (step 9): de-duplicate user-specified external sidecar data
  
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- TRX (step 10): write-only TRX handler sharing the read handler's utilities
  
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- TRX (step 11): intuitive -force interaction for augmenting a TRX dataset
  
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- TRX (step 12): consolidate read + write into a single TRX handler
  
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- Stage 17 step 1: implement the Grouping streamline-grouping data structure
  
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- Stage 17 steps 2-3: TRX groups/dpg read+write via the Grouping structure
  
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- Stage 17 step 4: encode connectome grouping via Grouping; text format preserved
  
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- TCK format: read Float16 (half-precision) vertex data
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- Docs: Add Float16 support to image and streamlines data
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- Add .zfib lossy streamline-compression format handler
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- Add qfib lossy tractography format handler
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- Accept all tractography formats in type_tracks arguments
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Commits on Jun 13, 2026
- Broadcast and enforce tractography non-finite value tolerance
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Commits on Jun 22, 2026
- Migrate C++ tractogram-export commands to the Tractogram class
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- Add DATASET::NAME sidecar export to tcksift2 and tcksample
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- Migrate tractography call sites from Reader<> to Tractogram
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- Make usage of SIFT2 weights in refactored tractogram handling explicit
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- Add arbitrary data field thresholding to tckedit
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- Migrate connectome2tck and other remaining to Tractogram
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- Support embedding sampled fixel values in tractogram datasets
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- Remove classes MR::DWI::Tractography::(Reader|Writer)
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- Refactor tractogram rendering with vertex classification and LOD buffers
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- Refactor tractogram LOD calculation for FoV-awareness and geometry-speci
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- Symmetrize vertex decimation gaps in tractogram LOD rendering
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- Expose vertex binary layout for GPU-accelerated tractography rendering
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- Conform .qfib/.zfib/.tt handlers to reference-software formats
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- Add cmake support for external tractography format reference data
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- Add reference-data validation tests for tckconvert
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- Various esoteric tweaks to newly supported tractogram formats
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- Normalize random_coord field names in gs_sidecar_trk test
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- Compact TRX offsets array to uint32 when vertex count permits
  
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- tckconvert: replace explicit transform options with coordinate-space options
  
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- Support naming a weight field of a piped tractogram via "::<field>"
  
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- Three tractography improvements outlined
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- Rename TractogramData{In,Out} argument types to TractogramSidecar{In,Out}
  
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- Restrict tractogram-sidecar self-reference to the empty-DATASET form only
  
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- Reject "::<field>" sidecar self-reference unless the tractogram is unique
  
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- Auto-document the tractogram-sidecar reference syntax in command help
  
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- tckconvert: rename coordinate-space options for clarity
  
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- Five CLI argument renaming and validation tasks completed sequentially
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- Enable TRX directory output and add -reference_image option to tckconver
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Commits on Jun 30, 2026
- Modulate mrview streamline thickness by tractogram sidecar data
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Commits on Jul 1, 2026
- Document tractography formats and restructure data format docs
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Commits on Sep 16, 2026
- tckconvert: Add example usages to help page
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- Warn / error on tractogram / sidecar size mismatch
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Commits

Commits on Jun 11, 2026

Commits on Jun 12, 2026

Commits on Jun 13, 2026

Commits on Jun 22, 2026

Commits on Jun 30, 2026

Commits on Jul 1, 2026

Commits on Sep 16, 2026