The EDDY QC tools

The EDDY QC framework consists of two different tools that automatically perform QC both at the single subject and study-wise level.

The tools can be called from the command line using eddy_quad and eddy_squad.

If you haven't already run EDDY on your data

The availability of different QC metrics depends on the exact options that EDDY was run with. This is determined by the EDDY QC tools based on what EDDY output files are present. E.g., metrics related to outlier slices are not calculated when the corresponding EDDY option has not been used. The following list contains the non-compulsory EDDY input parameters you may want to use when running EDDY to obtain more QC metrics.

Running QUAD

QUAD expects an EDDY output basename to identify the relevant output files that have been generated according to some user-specified options. If a feature, e.g., outliers detection and replacement, was not used, the outliers-related quality metrics will not be included in the final report nor added to the single-subject database. The most basic way to run eddy_quad after having pre-processed the dMRI dataset consists in running the following example command:

eddy_quad <eddy_output_basename> -idx <eddy_index_file> -par <eddy_acqparams_file> -m <nodif_mask> -b <bvals>

This will result in the creation of a new folder, called <eddy_output_basename>.qc. This will contain the single subject QC report and database, together with the slices included in the report stored as single image files.

List of input parameters

Output

Running SQUAD

SQUAD expects a list of single-subject QC folders generated by QUAD. The study-wise tool has been designed to allow maximum flexibility in terms of QC capabilities. The most basic way to run eddy_squad after having pre-processed the dMRI dataset consists in running the following example command:

eddy_squad <quad_folders>

This will result in the creation of a new folder, called squad. This will contain the study-wise QC report and database.

List of input parameters

The right way to format the text file listing the values associated to each subject is this:

The first line contains a string specifying the variable label; the second line contains either 0 or 1 to let SQUAD know whether the variable is categorical or continuous, respectively. Then there are n entries, where n is the number of subjects (i.e., QUAD folders) specified in the list file.

Output

 

eddyqc/UsersGuide (last edited 17:24:50 09-01-2019 by MatteoBastiani)