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Voxelwise dvars explodes with voxels with variance ~1e-19 #3487

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effigies opened this issue Jul 7, 2022 · 0 comments · Fixed by #3489
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Voxelwise dvars explodes with voxels with variance ~1e-19 #3487

effigies opened this issue Jul 7, 2022 · 0 comments · Fixed by #3489
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@effigies
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effigies commented Jul 7, 2022

Summary

In compute_dvars we remove zero-variance voxels:

nipype/nipype/algorithms/confounds.py

Lines 1045 to 1054 in 3e7e613

# Robust standard deviation (we are using "lower" interpolation
# because this is what FSL is doing
func_sd = (
np.percentile(mfunc, 75, axis=1, interpolation="lower")
- np.percentile(mfunc, 25, axis=1, interpolation="lower")
) / 1.349
if remove_zerovariance:
mfunc = mfunc[func_sd != 0, :]
func_sd = func_sd[func_sd != 0]

However, if func_sd is small but nonzero, this will propagate to diff_sdhat:

nipype/nipype/algorithms/confounds.py

Lines 1061 to 1063 in 3e7e613

# Compute (predicted) standard deviation of temporal difference time series
diff_sdhat = np.squeeze(np.sqrt(((1 - ar1) * 2).tolist())) * func_sd
diff_sd_mean = diff_sdhat.mean()

Which then can explode the values in

nipype/nipype/algorithms/confounds.py

Lines 1078 to 1080 in 3e7e613

diff_vx_stdz = np.square(
func_diff / np.array([diff_sdhat] * func_diff.shape[-1]).T
)

If sufficiently small, we will overflow float32.

Proposal

We should set a default threshold for "zerovariance". I think 1e-10 is more than small enough. In the example dataset I have, only one additional voxel is caught by this less stringent threshold, and would avoid the failure.

Will propose a fix soon, but wanted to give people a chance to comment.
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FIX: Add tolerance parameter to ComputeDVARS effigies/nipype
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@effigies