The AFQ-Browser data format#

AFQ-Browser supports input from two major tractometry software pipelines: AFQ and Tracula. However, data from other tractometry pipelines can also be used in AFQ-Browser, if the data is converted to the following data format specification.

Internally, AFQ-Browser represents its data in three different files:

1. A json file (streamlines.json) that contains a description of tract trajectories in the 3D space of the anatomy, and populates the “Anatomy” panel. This file has the following structure:

{"tract_name1":{"coreFiber":[[x1, y1, z1],
                              x2, y2, z2], ... ],
                "1":[[x1, y1, z1],
                     [x2, y2, z2], ...],
                "2":[[x1, y1, z1],
                      x1, y1, z1], ... ]},
"tract_name2":{"coreFiber":[[x1, y1, z1],...]...},

...
}

Where tract_name1 and tract_name2 can be replaced by keys that are the names of the tracts that you wish to represent. Within each tract, coreFiber is a required key, and subsequent numerical keys are not required. When tract representation (“core fiber”/”streamlines”) is selected in the GUI, either the core fibers for each tract are displayed, or all the numerically designated streamlines for that tract. Coordinates are kept in MNI space aligned to AC-PC.

2. A csv file (nodes.csv) that contains information about the tract profiles and populates the “Bundle details” panel. This table should have columns (and headers) named subjectID, tractID, and nodeID. The subjectID identifies a unique subject in your dataset, and it can take any string value you want (e.g., patient1), as long as it is consistent with the information in the subjects.csv file (see below). The tractID is the same key used in the streamlines.json file to identify the tracts (e.g., tract_name1, tract_name2, etc.). The nodeID runs from 0 to the n-1, where n is the number of nodes in the tract profile for that tract. Other columns in this table will hold the numerical values of statistics in this subject/tract/node/ combination. The headers for these columns can be named any string value that you would like (e.g., “FA”, “MD”, “my_statistic”, etc.).

3. A csv file (subjects.csv) that contains information about the subjects and populates the “Subject metadata” panel. This file is required to have a subjectID column that matches the subject identifiers used in nodes.csv (see above). It does not require any other columns, but can include any number of columns that describe the subjects in the study, holding numerical or string values.

To use data generated from another source, add these data files to the client/data folder in a copy of the site folder from the AFQ-Browser repo.

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