Script Overview

This page documents some important scripts that are installed with Datman, as well as how to use and configure them. All scripts discussed here can be found in Datman’s ‘bin’ folder.

dm_blacklist_rm

Description	Delete any files that have been blacklisted. Only removes data from the directories configured by BlacklistDel.
Environment Variables	None
Config Settings	BlacklistDel Paths
Additional Config Files	Blacklist
Additional Software Dependencies	None

dm_sftp

Description	Downloads scan zip files from an FTP Server. Note: The user running this script must have the sftp server in their ‘known_hosts’ file.
Environment Variables	None
Config Settings	Paths (zips, meta) FTP
Additional Config Files	None
Additional Software Dependencies	None

dm_link

Description	Apply the Datman naming convention to the raw zip files. Makes correctly-named symlinks in the ‘dicom’ folder that point to the original zip files in the ‘zips’ folder.
Environment Variables	None
Config Settings	Paths (dicom, zips, meta)
Additional Config Files	scans.csv
Additional Software Dependencies	None

dm_xnat_upload

Description	Uploads scan zip files from Datman’s ‘dicom’ directory to the configured XNAT server.
Environment Variables	XNAT_PASS: The XNAT user password. Overrides the config file if set. XNAT_USER: The XNAT username. Overrides the config file if set.
Config Settings	Paths (dicom, meta) XNAT IdMap (Optional)
Additional Config Files	None
Additional Software Dependencies	None

dm_xnat_extract

Description	Downloads scan data from the configured XNAT server and converts it to all configured file types.
Environment Variables	XNAT_PASS: The XNAT user password. Overrides the config file if set. XNAT_USER: The XNAT username. Overrides the config file if set.
Config Settings	Paths ExportInfo XNAT IdMap (Optional)
Additional Config Files	dcm2bids config
Additional Software Dependencies	dcm2niix (for nii/bids) dcm2bids (for bids) Slicer (for nrrd) MINC Tool Kit (for minc)

dm_link_shared_ids

Description	Links sessions from different studies as belonging to the same participant, based on the contents of a REDCap survey
Environment Variables	REDCAP_TOKEN: The redcap token to use for authentication. Ignored if defined in config files.
Config Settings	REDCap IdMap (Optional)
Additional Config Files	external-links
Additional Software Dependencies	None

dm_qc_report

Description	Generate QC metrics for the data in the study’s ‘nii’ folder. These will be put in the study’s ‘qc’ folder and can be displayed by the QC dashboard if it is installed.
Environment Variables	None
Config Settings	Paths (nii, qc, std, meta) Logging (Optional) Gold Standards
Additional Config Files	Checklist
Additional Software Dependencies	Matlab (R2014a) AFNI (2014) FSL (5.0.10) Newer versions may work, but no guarantees.

dm_redcap_scan_completed

Description	Retrieve redcap ‘scan completed’ survey data from a redcap server and push it to Datman’s QC dashboard database.
Environment Variables	None
Config Settings	Paths (meta) REDCap
Additional Config Files	None
Additional Software Dependencies	None

xnat_fetch_sessions

Description	Download XNAT sessions as raw scan zip files and deposit them in the study’s ‘zip’ folder.
Environment Variables	None
Config Settings	Paths (zips, meta) XNAT, only settings with the ‘XnatSource’ prefix Logging (Optional)
Additional Config Files	None
Additional Software Dependencies	None

dm_task_files

Description	Finds task files in the study’s ‘resources’ folder and symlinks them into the study’s ‘tasks’ folder with a standard name scheme.
Environment Variables	None
Config Settings	Paths (task, resources) Tasks
Additional Config Files	None
Additional Software Dependencies	None

dm_parse_faces

Description	Converts eprime text files for the FACES task into BIDS format .tsv files.
Environment Variables	None
Config Settings	Paths (task, nii)
Additional Config Files	None
Additional Software Dependencies	None

dm_update_standards

Description	Update the gold standards for a study. The scans chosen as gold standards should have correct header values that all new scans can be compared against.
Environment Variables	None
Config Settings	Paths (std)
Additional Config Files	None
Additional Software Dependencies	None