Other important files

This page describes some additional configuration files that Datman scripts may use.

dcm2bids.json

Used by: dm_xnat_extract.py

Location: the meta folder. By default this will be ${STUDY}/metadata.

This config file is used by dcm2bids to export raw dicom data to nifti format in the bids file structure. It should contain one entry for each scan that must be exported to nii format.

For more information see the dcm2bids official documentation

Example

This is a subset of the settings from one of our config files.

{"descriptions": [
    {
        "dataType": "anat",
        "modalityLabel": "T1w",
        "criteria": {
            "SeriesDescription": "*Sag_MPRAGE_T1*"
        }
    },
    {
        "dataType": "fmap",
        "modalityLabel": "epi",
        "customLabels": "acq-rest_dir-PA",
        "criteria": {
            "SeriesDescription": "*fMRI_FieldMap",
            "PhaseEncodingDirection": "j"
        },
        "sidecarChanges": {
            "B0FieldSource": "pepolar_rest_fmap"
        }
    },
    {
        "dataType": "fmap",
        "modalityLabel": "epi",
        "customLabels": "acq-dwi_dir-AP",
        "criteria": {
            "SeriesDescription": "DTI_FieldMap",
            "PhaseEncodingDirection": "j-"
        },
        "sidecarChanges": {
            "B0FieldSource": "pepolar_dwi_fmap"
        }
    }
]}

scans.csv

Used By: dm_link.py

Location: the meta folder. By default this will be ${STUDY}/metadata.

This file helps Datman apply a correctly formatted ID to scan zip files when the dicom headers do not contain a correct ID. Any scan zip file listed in scans.csv will have the name from the ‘target_name’ column applied instead of whatever has been entered into the dicom headers.

The ‘PatientName’ and ‘StudyID’ columns should be populated by their values from the dicom headers to help reduce the risk of trying to rename the wrong file. You can find these values with tools like dcmdump can retrieve these values.

Example

source_name      target_name      PatientName         StudyID
orig_zip_name1   intended_name1   dicom_PatientName1  dicom_StudyID1
...
orig_zip_nameN   intended_nameN   dicom_PatientNameN  dicom_StudyIDN

blacklist.csv

Used By: dm_blacklist_rm.py

Location: the meta folder. By default this will be ${STUDY}/metadata.

NOTE: This file is not used if the QC Dashboard is installed. The dashboard’s database stores this info instead.

This file holds the list of blacklisted scans for a study. It helps Datman identify scans which should not be processed.

The file should contain two comma-separated columns. The header should read ‘series,reason’. Each QC entry should go on it’s own line and should contain the scan’s root name (the file name, minus the series description and file extension) and the user’s comment about why the scan was blacklisted.

A scan root name appearing in this file indicates that it has been blacklisted and should not be used. That is, you should NOT add an entry for scans that pass QC, and you should NOT include these files when running processing pipelines.

Example

series,reason
STUDY_SITE_0000_01_01_TAG_00,user comment goes here

checklist.csv

Used By: Multiple Datman pre-processing pipelines.

Location: the meta folder. By default this will be ${STUDY}/metadata.

NOTE: This file is not used if the QC Dashboard is installed. The dashboard’s database stores this info instead.

This file holds a record of which sessions have had Quality Control (QC) performed. For some Datman scripts a session must undergo QC before the session will be processed.

When Datman generates a QC page for a session the name of the QC page gets added to checklist.csv. When a user is finished reviewing the data, they should add their initials in a space separated column to indicate it has been reviewed.

Example

qc_STUDY_CMH_0000_01.html CB
qc_STUDY_CMH_0001_01.html AA