dmri_bids_config: Auto-configure TRACULA to run on a BIDS-formatted dataset

NOTE: This is a new script that is currently only available in the development version of the FreeSurfer. You can download it from the development version and save it into your $FREESURFER_HOME/bin/ regardless of which version of FreeSurfer you are using.


dmri_bids_config --in <directory> --c <configfile>

This script will take as its input a BIDS-formatted study directory. It will parse the contents of this directory and it will output:

  1. A TRACULA configuration file: This file is needed to pre-process the DWI data, reconstruct tracts of interest, etc. with trac-all.

  2. A FreeSurfer Group Descriptor (FSGD) file: This file is needed to perform statistics on the output tract measures with mri_glmfit. It will be generated if the input BIDS directory contains a participants.tsv file.


Required arguments

At least one of the following two is required:

Optional arguments

After you run dmri_bids_config

It is important that you inspect the configuration file generated by this script to make sure that everything has been set up the way you intended. It is not always possible to guess the intentions of the investigator from the contents of BIDS directory structure. The TRACULA configuration file is a simple text file that you can edit as you wish before initiating data analysis.

The example configuration files and the tutorial explain in detail all the variables in the configuration file.

A few examples of situations where you may have to edit the configuration file:

See also

dmrirc, trac-all




If you use TRACULA, please cite:

If you use our measures of head motion, please cite:

If you use the longitudinal stream of TRACULA, please cite:

Reporting Bugs

Report bugs to < >


Anastasia Yendiki

dmri_bids_config (last edited 2021-12-08 22:43:57 by AnastasiaYendiki)