Configuration File

Some of the system wide options of NiPyPe can be configured using a configuration file. NiPyPe looks for the file in the local folder under the name nipype.cfg and in ~/.nipype.cfg (in this order). If an option will not be specified a default value will be assumed. The file is divided into following sections:

Logging

workflow_level

How detailed the logs regarding workflow should be (possible values: INFO and DEBUG; default value: INFO)

filemanip_level

How detailed the logs regarding file operations (for example overwriting warning) should be (possible values: INFO and DEBUG; default value: INFO)

interface_level

How detailed the logs regarding interface execution should be (possible values: INFO and DEBUG; default value: INFO)

log_directory

Where to store logs. (string, default value: home directory)

log_size

Size of a single log file. (integer, default value: 254000)

log_rotate

How many rotation should the log file make. (integer, default value: 4)

Execution

stop_on_first_crash

Should the workflow stop upon first node crashing or try to execute as many nodes as possible? (possible values: true and false; default value: false)

hash_method

Should the input files be checked for changes using their content (slow, but 100% accurate) or just their size and modification date (fast, but potentially prone to errors)? (possible values: content and timestamp; default value: content)

single_thread_matlab

Should all of the Matlab interfaces (including SPM) use only one thread? This is useful if you are parallelizing your workflow using IPython on a single multicore machine. (possible values: true and false; default value: true)

run_in_series

Should workflows be executed in series or parallel? (possible values: true and false; default value: false)

display_variable

What DISPLAY variable should all command line interfaces be run with. This is useful if you are using xnest or Xvfb and you would like to redirect all spawned windows to it. (possible values: any X server address; default value: not set)

use_relative_paths

Should the paths stored in results (and used to look for inputs) be relative or absolute. Relative paths allow moving the whole working directory around but may cause problems with simlinks. (possible values: true and false; default value: false)

remove_node_directories

Removes directories whose outputs have already been used up. Doesn’t work with IdentiInterface or any node that patches data through (without copying) (possible values: true and false; default value: false)

Example

[logging]
workflow_level = DEBUG

[execution]
stop_on_first_crash = true
hash_method = timestamp
display_variable = :1