Howto: debug

In this page we will list a few tricks for debugging a crash of the Connectome Mapper.

Most of the crashes will happen inside a Nipype workflow. Each crashing node will produce a nipype crashfile that can be inspected using the nipype_display_crash utility. Common reasons for a node crashing:

• Missing/wrong inputs. Each nodes defines a list of mandatory inputs and uses type validation (e.g. if it awaits an Integer, the input "bla" will give an error). Furthermore, existence of files is usually checked (flag 'exists=True' in input definition), trying to give a non-existing file as input will result in an error. Beware that the input path should usually be absolute, as the current working directory is changed for each node (e.g. a node give a relative path for one of it's output will probably lead to an error when connected to another node).
• Utility called by the node not existing on the system or not accessible. All the Nipype interfaces will suppose that the underlying utility (e.g. flirt for a fsl.FLIRT() node)can be called directly, meaning it is in the $PATH. Check the correct installation and configuration of the utilities.
• Problems during execution of the utility. Typically missing libraries needed by the utility will lead to an error during execution. Other errors are more rare due to the input validation of Nipype nodes but may happen if the Nipype interface is not on par with the utility version or if there is a problem in the input images for example.