ENH: Allow CompCor to skip initial volumes #2122
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@effigies - zero-padding will change the filter characteristics. if necessary this should be applied only to the pca components. on the other hand you can add N columns with a 1 at the location for every volume that is discarded (similar to ArtifactDetect). |
nipype/algorithms/confounds.py
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| if nvols: | ||
| ss_col = np.zeros((components.shape[0], 1), | ||
| dtype=filter_basis.dtype) | ||
| ss_col[:nvols] = 1 |
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I think we should model each volume with a separate regressor. Like artifacts in ArtDetect
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@satra Ah, you're right. The "steady state" column should be N columns with a single 1 in each. But to be clear, the data is truncated, the filter basis is constructed and applied before extracting the components. After that, the filter basis is zero-padded, to include in the GLM along with the components. Does that resolve the issue for you, or is there a problem I'm missing? |
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effigies
changed the title
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@satra I believe the CircleCI issues are unrelated to this PR. I also added docs to explain the behavior of this change and the high-pass filter. Let me know what you think. |
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Sorry. Realized a bug was being picked up downstream. Will check the box when ready. |
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@satra Sorry to bug you, but do you have any issues with this as it stands? |
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lgtm |
Follow-up to #2107.
Changes proposed in this pull request
NonSteadyStateDetectorinterfacefilter_basisfilter_basisandcomponentsare calculated on the truncated series, then zero-padded to fit original seriesTodo: