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nipreps / sdcflows

Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes
https://www.nipreps.org/sdcflows
Apache License 2.0
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MAINT: Make call to scipy.stats.mode compatible with scipy 1.11.0 #371

Closed HippocampusGirl closed 1 year ago

HippocampusGirl commented 1 year ago

Starting with scipy 1.11.0, scipy.stats.mode returns a scalar value for the mode instead of a one-element array. This change was foreshadowed in scipy version 1.9.0 with the addition of the keepdims parameter, with the eventual goal of setting it to false by default for consistency with other scipy.stats functions. This change is causing the _demean function to break, because it currently relies on indexing the resulting array.

NodeExecutionError: Exception raised while executing Node demean.

Traceback:
        Traceback (most recent call last):
          File "/usr/local/miniconda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/usr/local/miniconda/lib/python3.11/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
            out = function_handle(**args)
                  ^^^^^^^^^^^^^^^^^^^^^^^
          File "<string>", line 26, in _demean
        IndexError: invalid index to scalar variable.

See https://github.com/scipy/scipy/issues/16418 for the initial proposal and https://github.com/scipy/scipy/pull/17561 for the final change that is now breaking the _demean function.

This commit changes the indexing to be compatible with scipy 1.11.0 and other future versions. I have also tested this change with older scipy versions up to 0.17.1, which was released in 2016.

HippocampusGirl commented 1 year ago

The CI error seems to be a FreeSurfer license issue, so not related to the proposed change.

ERROR: FreeSurfer license file /opt/freesurfer/license.txt not found.
effigies commented 1 year ago

Pushed to a local branch to ensure CI has access to any secrets needed. https://app.circleci.com/pipelines/github/nipreps/sdcflows/1543/workflows/8fda487f-2ebc-46d4-82e5-eb99b8ec638f / #372.