From 0593ca4c5a34084340ef8ce8b0537cdaa94e0040 Mon Sep 17 00:00:00 2001
From: Sam Nastase <sam.nastase@gmail.com>
Date: Fri, 31 Jul 2020 13:44:34 -0400
Subject: [PATCH 1/2] Fix pairwise bootstrap to tolerate NaNs

---
 brainiak/isc.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/brainiak/isc.py b/brainiak/isc.py
index 27d14a223..4e6b48f76 100644
--- a/brainiak/isc.py
+++ b/brainiak/isc.py
@@ -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
@@ -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,
@@ -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 "
@@ -744,13 +749,13 @@ 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)
+                try:
+                    voxel_iscs = squareform(voxel_iscs, force='tomatrix')
+                except ValueError as e:
+                    raise Exception("Pairwise ISC input must be "
+                                    "distance-vector format") from e
                 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)

From a721dde7a836e39be7774e2735e3e56b96ff8e99 Mon Sep 17 00:00:00 2001
From: Sam Nastase <sam.nastase@gmail.com>
Date: Fri, 31 Jul 2020 14:19:19 -0400
Subject: [PATCH 2/2] Remove extraneous try/except error message (oops)

---
 brainiak/isc.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/brainiak/isc.py b/brainiak/isc.py
index 4e6b48f76..5250b7505 100644
--- a/brainiak/isc.py
+++ b/brainiak/isc.py
@@ -749,11 +749,7 @@ def bootstrap_isc(iscs, pairwise=False, summary_statistic='median',
             for voxel_iscs in iscs.T:
 
                 # Square the triangle and fill diagonal
-                try:
-                    voxel_iscs = squareform(voxel_iscs, force='tomatrix')
-                except ValueError as e:
-                    raise Exception("Pairwise ISC input must be "
-                                    "distance-vector format") from e
+                voxel_iscs = squareform(voxel_iscs, force='tomatrix')
                 np.fill_diagonal(voxel_iscs, 1)
 
                 # Shuffle square correlation matrix and get triangle