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run_defacing_script.md

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NAME

run_defacing.pl -- a script that creates defaced images for anatomical acquisitions specified in the Config module of LORIS.

SYNOPSIS

perl tools/run_defacing_script.pl [options]

Available options are:

-profile : name of the config file in ../dicom-archive/.loris_mri

-tarchive_ids: comma-separated list of MySQL TarchiveIDs

-verbose : be verbose

DESCRIPTION

This script will create defaced images for anatomical acquisitions that are specified in the Config module of LORIS.

METHODS

grep_FileIDs_to_deface($session_id_ref, @modalities_to_deface)

Queries the database for the list of acquisitions' FileID to be used to run the defacing algorithm based on the provided list of SessionID and Scan_type to restrict the search.

INPUTS:

  • $session_id_ref : array of SessionIDs to use when grepping FileIDs
  • @modalities_to_deface: array of Scan_type to use when grepping FileIDs

RETURNS: hash of matching FileIDs to be used to run the defacing algorithm organized in a hash as follows:

{0123}                          # sessionID key
    {flair}                     # flair scan type key
        {$FileID} = $File_path  # key = FileID; value = MINC file path
    {t1}                        # t1 scan type key
        {$FileID} = $File_path  # key = FileID 1; value = MINC file 1 path
        {$FileID} = $File_path  # key = FileID 2; value = MINC file 2 path

grep_candID_visit_from_SessionID($session_id)

Greps the candidate's CandID and the visit label corresponding to the SessionID given as input.

INPUT: the session ID to use to look for CandID and visit label

RETURNS: the candidate's CandID and the session visit label

check_if_deface_files_already_in_db($session_files, $session_id)

Checks whether there are already defaced images present in the database for the session.

INPUTS:

  • $session_files: list of files to deface
  • $session_id : the session ID to use to look for defaced images in files

RETURNS: 1 if there are defaced images found, 0 otherwise

grep_t1_ref_file($session_files, $ref_t1_scan_type)

Grep the first t1w image from $session_files to use it as a reference image for deface_minipipe.pl.

INPUTS:

  • $session_files : list of files to deface
  • $ref_t1_scan_type: LORIS scan type of the t1w file to use as a reference for deface_minipipe.pl

RETURNS: hash with information for the reference t1w image

determine_output_dir_and_basename($root_dir, $candID, $visit, $ref_file)

Determine the output directory path and basename to be used by deface_minipipe.pl.

INPUTS:

  • $root_dir: root directory (usually a temporary directory where defaced outputs will be created)
  • $candID : candidate's CandID
  • $visit : candidate's visit label
  • $ref_file: hash with information about the reference t1 file to use to deface

RETURNS:

  • $output_basedir : output base CandID/VisitLabel directory where defaced images will be created
  • $output_basename: basename to be used to create the _deface_grid_0.mnc file

deface_session($ref_file, $session_files, $output_basename)

Function that will run deface_minipipe.pl on all anatomical images of the session and will return all defaced outputs in a hash.

INPUTS:

  • $ref_file : hash with info about the reference t1w file used to deface
  • $session_files : list of other files than the reference t1w file to deface
  • $output_basename: output basename to be used by deface_minipipe.pl

RETURNS: hash of defaced images with relevant information necessary to register them

fetch_defaced_files($ref_file, $session_files, $output_basename)

Function that will determine the name of the defaced outputs and check that the defaced outputs indeed exists in the file system. If all files are found in the filesystem, it will return a hash with all information necessary for registration of the defaced image.

INPUTS:

  • $ref_file : hash with info about the reference t1w file used to deface
  • $session_files : list of other files than the reference t1w file to deface
  • $output_basename: output basename to be used by deface_minipipe.pl

RETURNS: hash of defaced images with relevant information necessary to register them

register_defaced_files($defaced_images)

Registers the defaced images using register_processed_data.pl.

INPUT: hash with the defaced images storing their input FileID and scan type

create_defaced_scan_type($scan_type)

Function that inserts a new scan type in mri_scan_type if the scan type does not already exists in mri_scan_type.

INPUT: the scan type to look for or insert in the mri_scan_type table

LICENSING

License: GPLv3

AUTHORS

LORIS community loris.info@mcin.ca and McGill Centre for Integrative Neuroscience