Andrea Urru: main author.
Valentin Comte: contributor.
To run the perinatal pipeline you will need to download and install the dHCP pipeline.
Once the dHCP pipeline has been installed, you will need to install ANTs.
After these steps, you can clone this repository and its content in the dhcp-structural-pipeline folder previously created. After running the setup_perinatal.sh script you will be able to run the pipeline using the following command line:
./perinatal-pipeline.sh <path/to/raw/images> <path/to/demographics/csv/file> <fetneo flag (0 for fetal, 1 for neonatal)> <multisubject altas to use (ANDREAs/ALBERTs)>
The demorgraphics file should be structured with a first column for the ID, a second column for their gestational age at fetal acquisition (if applicable), and a third column for their gestational age at neonatal acquisition (if applicable).
The raw files should be named fet{ID} or neo{ID}. based on their developmental stage, and put in a directory named after their image type (T2/T1), eg., <path/to/raw/images>/T2/fet037.nii.gz.