diff --git a/openbr/core/core.cpp b/openbr/core/core.cpp
index fae1184..cea16f1 100644
--- a/openbr/core/core.cpp
+++ b/openbr/core/core.cpp
@@ -453,14 +453,23 @@ void br::Convert(const File &fileType, const File &inputFile, const File &output
         const FileList targetFiles = TemplateList::fromGallery(target).files();
         const FileList queryFiles = TemplateList::fromGallery(query).files();
 
-        if (targetFiles.size() != m.cols || queryFiles.size() != m.rows)
+        if ((targetFiles.size() != m.cols || queryFiles.size() != m.rows)
+            && (m.cols != 1 || targetFiles.size() != m.rows || queryFiles.size() != m.rows))
             qFatal("Similarity matrix and file size mismatch.");
 
         QSharedPointer<Output> o(Factory<Output>::make(outputFile));
         o->initialize(targetFiles, queryFiles);
 
-        for (int i=0; i<queryFiles.size(); i++)
-            for (int j=0; j<targetFiles.size(); j++)
+        if (targetFiles.size() != m.cols)
+        {
+            MatrixOutput   * mOut = dynamic_cast<MatrixOutput *>(o.data());
+            if (mOut)
+                mOut->data.create(queryFiles.size(), 1, CV_32FC1);
+        }
+
+        o->setBlock(0,0);
+        for (int i=0; i < m.rows; i++)
+            for (int j=0; j < m.cols; j++)
                 o->setRelative(m.at<float>(i,j), i, j);
     } else {
         qFatal("Unrecognized file type %s.", qPrintable(fileType.flat()));
diff --git a/openbr/core/eval.cpp b/openbr/core/eval.cpp
index 2406a01..15246cc 100644
--- a/openbr/core/eval.cpp
+++ b/openbr/core/eval.cpp
@@ -65,9 +65,26 @@ static float getTAR(const QList<OperatingPoint> &operatingPoints, float FAR)
     return m * FAR + b;
 }
 
+// Decide whether to construct a normal mask matrix, or a pairwise mask by comparing the dimensions of
+// scores with the size of the target and query lists
+static cv::Mat constructMatchingMask(const cv::Mat & scores, const FileList & target, const FileList & query, int partition=0)
+{
+    // If the dimensions of the score matrix match the sizes of the target and query lists, construct a normal mask matrix
+    if (target.size() == scores.cols && query.size() == scores.rows)
+        return BEE::makeMask(target, query, partition);
+    // If this looks like a pairwise comparison (1 column score matrix, equal length target and query sets), construct a
+    // mask for that
+    else if (scores.cols == 1 && target.size() == query.size()) {
+        return BEE::makePairwiseMask(target, query, partition);
+    }
+    // otherwise, we fail
+    else
+        qFatal("Unable to construct mask for %d by %d score matrix from %d element query set, and %d element target set ", scores.rows, scores.cols, query.length(), target.length());
+}
+
 float Evaluate(const cv::Mat &scores, const FileList &target, const FileList &query, const QString &csv, int partition)
 {
-    return Evaluate(scores, BEE::makeMask(target, query, partition), csv);
+    return Evaluate(scores, constructMatchingMask(scores, target, query, partition), csv);
 }
 
 float Evaluate(const QString &simmat, const QString &mask, const QString &csv)
@@ -93,8 +110,9 @@ float Evaluate(const QString &simmat, const QString &mask, const QString &csv)
         // Use the galleries specified in the similarity matrix
         if (target.isEmpty()) qFatal("Unspecified target gallery.");
         if (query.isEmpty()) qFatal("Unspecified query gallery.");
-        truth = BEE::makeMask(TemplateList::fromGallery(target).files(),
-                              TemplateList::fromGallery(query).files());
+
+        truth = constructMatchingMask(scores, TemplateList::fromGallery(target).files(),
+                                              TemplateList::fromGallery(query).files());
     } else {
         File maskFile(mask);
         maskFile.set("rows", scores.rows);
diff --git a/openbr/plugins/output.cpp b/openbr/plugins/output.cpp
index 9f8301b..1ad0995 100644
--- a/openbr/plugins/output.cpp
+++ b/openbr/plugins/output.cpp
@@ -371,7 +371,7 @@ class evalOutput : public MatrixOutput
         if (data.data) {
             const QString csv = QString(file.name).replace(".eval", ".csv");
             if ((Globals->crossValidate == 0) || (!crossValidate)) {
-                Evaluate(data, BEE::makeMask(targetFiles, queryFiles), csv);
+                Evaluate(data,targetFiles, queryFiles, csv);
             } else {
                 QFutureSynchronizer<float> futures;
                 for (int i=0; i<Globals->crossValidate; i++)