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make ciftify_meants work with wb_command versions ? 1.3. #153

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edickie opened this issue May 11, 2021 · 1 comment
Open

make ciftify_meants work with wb_command versions ? 1.3. #153

edickie opened this issue May 11, 2021 · 1 comment

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@edickie
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edickie commented May 11, 2021

The problem
Currently: https://github.com/edickie/ciftify/blob/master/ciftify/bin/ciftify_meants.py [line 100]

ciftify.utils.run(['wb_command', '-cifti-parcellate',
            settings.func.path, settings.seed.path,
            'COLUMN', tmp_parcelated, '-include-empty'])

BUT as of wb_command 1.4 (I believe) "'-include-empty' is deprecated but is now the default behaviour". However the deprecation warning kills the computation...

So ciftify needs to:

  1. detect the version of wb_command (actually I think we do this in ciftify.utils.wb_command_version()
  2. change behaviour of above section to remove '-include-empty'. if version is >=1.4
  3. test code with multiple versions of wb_command (note: I believe the CI is already set up for this?)
@marcelzwiers
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What would be the recommended workbench version for ciftify?

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