• dmri_bids_config

Index

Name

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

Usage

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.

Arguments

Required arguments

• --in <directory>

  Path to the input data (the top-level BIDS directory for the study, not a single subject or session directory)

At least one of the following two is required:

• --c <file>	Output configuration file that specifies DWI inputs and analysis options for TRACULA
  --f <file>	Output FSGD file that specifies subject-specific continuous and discrete variables for linear regression analyses (Default: append .fsgd to the argument of --c)

Optional arguments

• --fsdir <directory>	FreeSurfer SUBJECTS_DIR for this study (This must be specified, either here or with: setenv SUBJECTS_DIR ...)
  --trdir <directory>	Output TRACULA directory for this study (If not specified, TRACULA will use the FreeSurfer SUBJECTS_DIR)
  --acq <name>	Only use DWI scans collected with this acquisition (The name of the NIfTI volumes in BIDS must include the string acq- followed by this name)

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:

• If the subject names under your FreeSurfer SUBJECTS_DIR directory do not match the subject/session names that they have in the BIDS structure, then you have to edit the configuration file to make sure that the subjlist variable contains the subject names in your SUBJECTS_DIR (i.e., the names that you used when you ran recon-all on the structural images).

• If this is a longitudinal study, then the subjlist and baselist variables in the configuration file must match, respectively, the time point and base names in your SUBJECTS_DIR (i.e., the names that you used when you ran the longitudinal stream of recon-all on the structural images).

• If at least one of your subjects has DWIs from multiple sessions (this means multiple visits, not multiple DWI scans in the same visit), then we will assume that this is a longitudinal study and the configuration file will be set up to run the longitudinal stream of TRACULA. If this is not the case and, for example, you only want to use one session from each subject, then you have to edit the configuration file to remove all entries related to the unwanted sessions, and to remove the baselist variable entirely.

• If you collected multiple DWI scans in the same scan session but these should not be analyzed together (e.g., you ran different sequences that you want to compare or to use for different analyses), you should check the configuration file to make sure that it contains only the DWI scans that you intend to use. (This can be also controlled with the --acq command-line argument, assuming that an acquisition string is included in the names of the NIfTI volumes in the BIDS structure.)

• If there are multiple possibilities for how B0 inhomogeneity correction can be performed (e.g., the DWIs were collected with multiple phase-encode directions, but separate field mapping scans were also collected), you should inspect the configuration file to make sure that corrections will be performed with the method of your choice.
• You may want to change settings of the downstream analysis with TRACULA (e.g., reconstruct only a few tracts of interest and not all 42).
• These are just a few examples. Please inspect the configuration file after it is generated and before it is used for analysis, even if none of the above applies to you.

See also

dmrirc, trac-all

Links

TRACULA

References

If you use TRACULA, please cite:

• Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy. Yendiki A, Panneck P, Srinivasan P, Stevens A, Zöllei L, Augustinack J, Wang R, Salat D, Ehrlich S, Behrens T, Jbabdi S, Gollub R and Fischl B (2011). Front. Neuroinform. 5:23. doi: 10.3389/fninf.2011.00023

• Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data. Maffei C, Lee C, Planich M, Ramprasad M, Ravi N, Trainor D, Urban Z, Kim M, Jones R, Henin A, Hofmann S, Pizzagalli D, Auerbach R, Gabrieli J, Whitfield-Gabrieli S, Greve D, Haber N, Yendiki A (2021). NeuroImage 245:118706.

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

• Spurious group differences due to head motion in a diffusion MRI study. Yendiki A, Koldewyn K, Kakunoori S, Kanwisher N, Fischl B (2014). NeuroImage 88:79–90.

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

• Joint reconstruction of white-matter pathways from longitudinal diffusion MRI data with anatomical priors. Yendiki A, Reuter, M, Wilkens P, Rosas H D, Fischl B (2016). NeuroImage 127:277–286.

Reporting Bugs

Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >

Author/s

Anastasia Yendiki