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Hippocampal feature post-processing

This section describes how to generate raw and normalized features sampled along hippocampal surfaces generated by HippUnfold.

Define your directories: Hippocampus

zbrains requires input and output directories:

root_path points to the BIDS-format dataset that stores imaging data rawdir contains the raw imaging data micapipedir contains the output of micapipe previously run on the BIDS dataset hippdir contains the output of hippunfold previously run on the BIDS dataset outdir points to the directory that will hold zbrains outputs

In practice, these should be declared as variables:

# path for dataset in BIDS structure
root_path=/path/to/BIDS_dataset
rawdir=${root_path}/rawdata
micapipedir=${root_path}/derivatives/micapipe_folder
hippdir=${root_path}/derivatives/hippunfold_folder
outdir=${root_path}/derivatives/zbrains_folder

Run hippocampal post-processing

After defining our directories, we can move on to processing our first patient. Let's declare which patient we want to process (with their ID in the BIDS directory, omitting the 'sub-' and the session that should be processed if necessary).

id=PX001
ses=01

To process the subject, we can specify the command as follows:

zbrains -sub "$id" -ses "$ses" \
    -rawdir "${rawdir}" \
    -micapipedir "${micapipedir}" \
    -hippdir "${hippdir}" \
    -outdir "${outdir}" \
    -run proc \
    -struct hippocampus \
    -verbose 2

This will generate surface-based hippocampal features at the default smoothing (2mm) and mesh resolution (both 2mm and 0p5m template resolution) for all available modalities.

Customize your zbrains run!

A list of options and flags can be specified for a more personalized run of zbrains. Check out the help menu zbrains -help