Configuration

The main nodes in the pipelines are configurable through a configuration file.

We recommend using the YAML (https://en.wikipedia.org/wiki/YAML) format for this file.

To change the default value of a node parameter you have to add to the configuration file an entry for the value you want, as in: <node_name>.<parameter_name>: <value>

For example, let's say we have a spm.Normalize12 node named anat_warp in one of the workflows. We want to set the value of the parameter bias_regularization to 0.1. The entry should be:

anat_warp.bias_regularization: 0.1

The most direct way of checking the names of the nodes defined in Neuro_Pypes, is by looking into the source code. You can also have a look at the default configuration file where we list the settings for the main nodes in each workflow. In addition we have added a "Related settings" section for each workflow description where we list the most important configuration settings, taken from this file.