These are dHCP inspired processing pipelines for neonatal MRI data.
This repository can go inside the /code folder within of a BIDS "studyfolder".
The data is organized in the same way as the 2nd data release for the dHCP and expects the NIfTI sourcedata files to be located in the BIDS folder /sourcedata (SIC!).
Processed data/Processing pipelines store results in /derivatives
The processing pipelines and processing scripts are organised as followed:
To organise the data in BIDS datastructure format
To process the sMRI data within the framework of the dhcp-structural-pipeline. These includes neonatal segmentation with DrawEM and surface generation and analysis.
NOTE - current version of DrawEM version 1.3 has incorporated optional segmentation according to the M-CRIB_2.0 atlas
Various LUTs for anatomical parcellations for the ALBERTs and M-CRIB atlases. Also for conversions into MRtrix's 5TT format.