This library provides functions to import MRI features and metadata into an I2B2 DB schema.
MRI features are CSV files containing the features such as volumes of white matter and gray matter computed by the MRI preprocessing pipeline.
MRI metadata are stored into the Data Catalog database and usually come from DICOM file headers but also XML or JSON files, depending on the organisation of the incoming MRI scans.
Run: pip install i2b2_import
To import brain features (and/or other observations) from a CSV file, use:
features_csv_import.csv2db(file_path, i2b2_conn, dataset, config):
Import brain features and other observation facts data from a CSV file into the I2B2 DB schema.
* param file_path: Path to the CSV file.
* param i2b2_db_url: URL of the I2B2 DB.
* param dataset: Data set name.
* param config: A few settings. It is a dictionary that accepts the following fields:
- pid_in_vid: Rarely, a data set might mix patient IDs and visit IDs. E.g. : LREN data. In such a case, you
to enable this flag. This will try to split PatientID into VisitID and PatientID.
- sid_by_patient: Rarely, a data set might use study IDs which are unique by patient (not for the whole study).
E.g.: LREN data. In such a case, you have to enable this flag. This will use PatientID + StudyID as a sessionID.
* param regions_name_file: CSV file containing the abbreviated regions name in the first column and the full names
in the second column.
or from a folder:
features_csv_import.folder2db(folder, i2b2_conn, dataset, config):
Import brain features and other observation facts data from a folder containing CSV files into the I2B2 DB schema.
* param folder: Folder path
* param i2b2_db_url: URL of the I2B2 DB.
* param dataset: Data set name.
* param config: A few settings. It is a dictionary that accepts the following fields:
- pid_in_vid: Rarely, a data set might mix patient IDs and visit IDs. E.g. : LREN data. In such a case, you
to enable this flag. This will try to split PatientID into VisitID and PatientID.
- sid_by_patient: Rarely, a data set might use study IDs which are unique by patient (not for the whole study).
E.g.: LREN data. In such a case, you have to enable this flag. This will use PatientID + StudyID as a sessionID.
* param regions_name_file: CSV file containing the abbreviated regions name in the first column and the full names
in the second column.
To import metadata from the data-catalog-db, use:
data_catalog_import.catalog2i2b2(data_catalog_conn, i2b2_conn):
Import meta data from the Data Catalog DB to the I2B2 schema.
* param data_catalog_conn: Connection to the Data Catalog DB.
* param i2b2_db_url: URL of the I2B2 DB.
To import metadata from extra files (XML, JSON, ...), use:
ppmi_xml_import.meta2i2b2(file_path, db_conn, dataset):
Import meta-data from a file into the I2B2 schema.
* param file_path: File (XML, JSON, ...) containing meta-data for a given dataset (PPMI, EDSD, ...).
* param i2b2_db_url: Connection to the I2B2 DB.
* param dataset: Dataset ID (each dataset uses its own meta-data files format)
or from a folder:
ppmi_xml_import.folder2db(folder, db_conn, dataset):
Import meta-data from files from a given folder (recursive) and for a given dataset into the I2B2 schema.
* param folder: Folder containing meta-data files for a given dataset.
* param i2b2_db_url: URL of the I2B2 DB.
* param dataset: Dataset ID (each dataset uses its own meta-data files format)
Open the tests directory and run ./test.sh.
NOTE: Docker is needed.
Run ./build.sh.
Run ./publish.sh.
(This builds the project prior to pushing it).
This work has been funded by the European Union Seventh Framework Program (FP7/20072013) under grant agreement no. 604102 (HBP)
This work is part of SP8 of the Human Brain Project (SGA1).