AFNI automask broken (urgent help would be great)

[Michael]

AFNI Automask does not generate output strings correctly and string pattern %s is literally used in the generated command:

Given:

automask = afni.Automask()

automask.inputs.in_file = '/path/to/my_file.nii.gz'

automask.inputs.dilate = 1

automask.inputs.outputtype = "NIFTI_GZ"

No longer generate (automask.cmdline):

3dAutomask -apply_prefix /path/to/my_file_masked.nii.gz -dilate 1 -prefix /path/to/my_file_mask.nii.gz /path/to/my_file.nii.gz

But this nonviable command instead:

3dAutomask -apply_prefix %s_masked -dilate 1 -prefix %s_mask /path/to/my_file.nii.gz

[Satrajit Ghosh]

hi michael,

do you mind trying this branch?

PR: https://github.com/nipy/nipype/pull/693

branch: https://github.com/chrisfilo/nipype/tree/enh/afni_refactor

cheers,

satra

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[Michael]

Hi Satra,

Thank you so much for such a quick reply, this is for 50+ subjects to process urgently and this issue stuck my whole pipeline. I actually very luckily just found something which worked, i submitted a PR right now but my fix may be a hack.

[Michael]

Latest nipype master fixed it! Amazing help, thanks!

[Michael]

I can confirm everything's working great, thanks again for the fantastic support

[Chris Filo Gorgolewski]

Awesome. Could you check if it's still working on the PR: https://github.com/nipy/nipype/pull/693 ?

[Michael]

Ok i'll do that!

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[Michael]

Yes works fine. Sorry got entangled in between git commands and virtual envs

On Saturday, October 19, 2013 8:45:00 PM UTC-4, Michael wrote:

Ok i'll do that!

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