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Fix pairwise bootstrap to tolerate NaNs #475

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Merged
mihaic merged 4 commits into from
Aug 31, 2020
Merged

Fix pairwise bootstrap to tolerate NaNs #475

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0593ca4
Fix pairwise bootstrap to tolerate NaNs
snastase Jul 31, 2020
a721dde
Remove extraneous try/except error message (oops)
snastase Jul 31, 2020
c360972
Merge branch 'master' into isc-boot-fix
snastase Aug 16, 2020
62eb367
Merge branch 'master' into isc-boot-fix
mihaic Aug 17, 2020
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15 changes: 8 additions & 7 deletions brainiak/isc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
as statistical tests designed specifically for ISC analyses.

The implementation is based on the work in [Hasson2004]_, [Kauppi2014]_,
[Simony2016]_, and [Chen2016]_.
[Simony2016]_, [Chen2016]_, and [Nastase2019]_.

.. [Chen2016] "Untangling the relatedness among correlations, part I:
nonparametric approaches to inter-subject correlation analysis at the
Expand All @@ -41,6 +41,11 @@
during narrative comprehension.", E. Simony, C. J. Honey, J. Chen, O.
Lositsky, Y. Yeshurun, A. Wiesel, U. Hasson, 2016, Nature Communications,
7, 12141. https://doi.org/10.1038/ncomms12141

.. [Nastase2019] "Measuring shared responses across subjects using
intersubject correlation." S. A. Nastase, V. Gazzola, U. Hasson,
C. Keysers, 2019, Social Cognitive and Affective Neuroscience, 14,
667-685. https://doi.org/10.1093/scan/nsz037
"""

# Authors: Sam Nastase, Christopher Baldassano, Qihong Lu,
Expand Down Expand Up @@ -405,7 +410,7 @@ def _check_isc_input(iscs, pairwise=False):
# Check if incoming pairwise matrix is vectorized triangle
if pairwise:
try:
test_square = squareform(iscs[:, 0])
test_square = squareform(iscs[:, 0], force='tomatrix')
n_subjects = test_square.shape[0]
except ValueError:
raise ValueError("For pairwise input, ISCs must be the "
Expand Down Expand Up @@ -751,13 +756,9 @@ def bootstrap_isc(iscs, pairwise=False, summary_statistic='median',
for voxel_iscs in iscs.T:

# Square the triangle and fill diagonal
voxel_iscs = squareform(voxel_iscs)
voxel_iscs = squareform(voxel_iscs, force='tomatrix')
np.fill_diagonal(voxel_iscs, 1)

# Check that pairwise ISC matrix is square and symmetric
assert voxel_iscs.shape[0] == voxel_iscs.shape[1]
assert np.allclose(voxel_iscs, voxel_iscs.T)

# Shuffle square correlation matrix and get triangle
voxel_sample = voxel_iscs[subject_sample, :][:, subject_sample]
voxel_sample = squareform(voxel_sample, checks=False)
Expand Down