Eddy-Wrapper does not work properly

[JensNRAD]

Hi,

thanks for the great Framework.

I think there are two bugs in the FSL Eddy wrapper.

[319] in_topup = File(exists=True, desc='Base name for output files from topup', argstr='--topup=%s' )

does not work correctly, because eddy just expects a base name which it uses for two files (basename_fieldcoef.nii.gz and basename_movpar.txt). A quick fix is to set exists=False.

The second bug is in the output check.
[368] outputs['out_parameter'] = '%s..eddy_parameters' % self.inputs.out_base

it should read:
[368] outputs['out_parameter'] = '%s.eddy_parameters' % self.inputs.out_base
(Just one dot between %s and eddy_parameters.

[satra]

thanks for this. could you please send a PR with the fixes?

also a question regarding the first bug. doesn't in_topup refer to two files that are output from topup? if so, i think the interface will need to take those files separately from a workflow perspective and use the basename only.

@oesteban - fyi

[oesteban]

Thanks, I am currently finishing things in a project, so I will look at it very soon :).

[JensNRAD]

Yes, "in_topup" refers to the two files that are output from topup.

I am not sure how to modify the interface, so it takes just the basename as an input and then checks for the presence of both files. Can you point me to an example interface, where this has been implemented. Then I can change it and send a PR.

[chrisgorgo]

I think the most flexible way to do this is to remove in_topup and replace
it with "fieldcoef" and "movpar" inputs. Then overload _run_interface to
copy/rename the input fieldcoef and movpar files to whatever pattern eddy
expects. This way we enable straighforward connection between topup and
eddy as well as enable users to easily intercept and modify fieldcoef and
movpar files. Similar scheme has been used for bedpostx and probtractx.

On Thu, Jan 23, 2014 at 11:40 PM, JensNRAD [email protected] wrote:

Yes, "in_topup" refers to the two files that are output from topup.

I am not sure how to modify the interface, so it takes just the basename
as an input and then checks for the presence of both files. Can you point
me to an example interface, where this has been implemented. Then I can
change it and send a PR.

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