Node picopdfs failed to run on host

[Elena Molina]

Hi all,

I am running the create_camino_dti_pipeline and I have the following problem with the PicoPDFsInputSpect:

traits.trait_errors.TraitError: The 'luts' trait of a PicoPDFsInputSpec instance must be a list of from 1 to 3 items which are an existing file name, but a value of <type 'str'> was specified.

Any suggestions? Thanks.

Cheers,

Elena

[Chris Filo Gorgolewski]

You are most likely feeding wrong values to PicoPDFs's "luts"  input. As the documentation states http://nipy.sourceforge.net/nipype/interfaces/generated/nipype.interfaces.camino.dti.html#picopdfs (and the error confirms) it should be a list of existing filenames. My bet is that you are setting it to '/path/to/my/luts' instead of ['/path/to/my/luts'].

Best,

Chris

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[Elena Molina]

Hi Chris,

Thank you for your answer. I tried the example with  ['/path/to/my/luts'] and it works but I don´t know how can i fix it in the diffusion.py script that I am using.

from nipype.workflows.dmri.camino.diffusion import create_camino_dti_pipeline

    Workflow for applying PICo

    """

    tractography.connect([(bet, trackpico,[("mask_file","seed_file")])])

    tractography.connect([(fsl2scheme, dtlutgen,[("scheme","scheme_file")])])

    tractography.connect([(dtlutgen, picopdfs,[("dtLUT","luts")])])

    tractography.connect([(dtifit, picopdfs,[("tensor_fitted","in_file")])])

    tractography.connect([(picopdfs, trackpico,[("pdfs","in_file")])])

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[Chris Filo Gorgolewski]

I see the problem now. I think I found a fix. Could you try if this branch:

https://github.com/chrisfilo/nipype/tree/fix/camino_multipath (for more detail here's the pull request: https://github.com/nipy/nipype/pull/810)

resolves the issue for you?

Best,

Chris