TRX Format Specification

This page documents the on-disk layout and data model of the TRX tractography format. TRX-cpp is an implementation of this specification; the authoritative specification repository is at tee-ar-ex/trx-spec.

General layout

A TRX file is either an uncompressed or compressed ZIP archive, or a plain directory. In both cases the internal structure is identical: the file hierarchy describes the data, and filename components encode metadata.

• Each file’s basename is the name of the metadata field.

• Each file’s extension is the dtype (e.g., float16, uint32).

• Multi-component arrays encode the number of components between the basename and the extension (e.g., positions.3.float16 has 3 components per row). Single-component arrays may omit this field for readability.

All arrays use C-style (row-major) memory layout and little-endian byte order.

Compression is optional. Use ZIP_STORE for uncompressed storage; use ZIP_DEFLATE if compression is desired. Compressed files must be decompressed before memory-mapping.

Header

header.json is a JSON dictionary with the following fields:

Field	Type	Description
VOXEL_TO_RASMM	4×4 array of float	Affine from voxel to RAS+
DIMENSIONS	list of 3 uint16	Reference image grid size
NB_STREAMLINES	uint32	Number of streamlines
NB_VERTICES	uint64	Total number of vertices

The header is primarily for human readability and downstream compatibility checks. The authoritative array sizes come from the data arrays themselves.

Arrays

positions (positions.float16 / positions.float32 / positions.float64)

All streamline vertices as a contiguous C array of shape (NB_VERTICES, 3). Stored in RAS+ world space (millimeters), matching the MRtrix3 .tck convention.

offsets (offsets.uint32 / offsets.uint64)

Prefix-sum index of length NB_STREAMLINES + 1. Element i is the index in positions of the first vertex of streamline i. The final element is a sentinel equal to NB_VERTICES.

Streamline length: length_i = offsets[i+1] - offsets[i].

dpv — data per vertex (dpv/<name>.<dtype>)

Shape (NB_VERTICES, 1) or (NB_VERTICES, N). Values are aligned with positions row-by-row.

dps — data per streamline (dps/<name>.<dtype>)

Shape (NB_STREAMLINES, 1) or (NB_STREAMLINES, N). Values are aligned with streamlines.

groups (groups/<name>.uint32)

Variable-length index arrays. Each file lists the 0-based indices of streamlines belonging to the named group. All indices must satisfy 0 ≤ id < NB_STREAMLINES. Groups are non-exclusive: a streamline may appear in multiple groups.

dpg — data per group (dpg/<group>/<name>.<dtype>)

Shape (1,) or (N,). Each subdirectory corresponds to one group. Not all metadata fields need to be present in every group.

Accepted dtypes

Signed	Unsigned	Float
int8	uint8	float16
int16	uint16	float32
int32	uint32	float64
int64	uint64

Example structure

OHBM_demo.trx
├── dpg/
│   ├── AF_L/
│   │   ├── mean_fa.float16
│   │   ├── shuffle_colors.3.uint8
│   │   └── volume.uint32
│   ├── AF_R/  CC/  CST_L/  CST_R/  SLF_L/  SLF_R/
├── dpv/
│   ├── color_x.uint8
│   ├── color_y.uint8
│   ├── color_z.uint8
│   └── fa.float16
├── dps/
│   ├── algo.uint8
│   ├── algo.json
│   ├── clusters_QB.uint16
│   ├── commit_colors.3.uint8
│   └── commit_weights.float32
├── groups/
│   ├── AF_L.uint32
│   ├── AF_R.uint32
│   ├── CC.uint32
│   ├── CST_L.uint32
│   ├── CST_R.uint32
│   ├── SLF_L.uint32
│   └── SLF_R.uint32
├── header.json
├── offsets.uint64
└── positions.3.float16