diff --git a/openbr/core/bee.cpp b/openbr/core/bee.cpp
index 8682215..940ddf2 100644
--- a/openbr/core/bee.cpp
+++ b/openbr/core/bee.cpp
@@ -180,16 +180,17 @@ Mat BEE::readMat(const br::File &matrix, QString *targetSigset, QString *querySi
     return result;
 }
 
-template <typename T>
-void writeMatrix(const Mat &m, const QString &matrix, const QString &targetSigset, const QString &querySigset)
+void BEE::writeMat(const Mat &m, const QString &matrix, const QString &targetSigset, const QString &querySigset)
 {
-    if (m.type() != OpenCVType<T,1>::make()) qFatal("Invalid matrix type.");
+    bool isMask = false;
+    if (m.type() == OpenCVType<BEE::Mask_t,1>::make())
+        isMask = true;
+    else if (m.type() != OpenCVType<BEE::Simmat_t,1>::make())
+        qFatal("Invalid matrix type, .mtx files can only contain single channel float or uchar matrices.");
 
-    int elemSize = sizeof(T);
-    QString matrixType;
-    if      (elemSize == 1) matrixType = "B";
-    else if (elemSize == 4) matrixType = "F";
-    else                    qFatal("Invalid element size.");
+    int elemSize = isMask ? sizeof(BEE::Mask_t) : sizeof(BEE::Simmat_t);
+
+    QString matrixType = isMask ? "B" : "F";
 
     char buff[4];
     QFile file(matrix);
@@ -215,16 +216,6 @@ void writeMatrix(const Mat &m, const QString &matrix, const QString &targetSigse
     file.close();
 }
 
-void BEE::writeSimmat(const Mat &m, const QString &simmat, const QString &targetSigset, const QString &querySigset)
-{
-    writeMatrix<Simmat_t>(m, simmat, targetSigset, querySigset);
-}
-
-void BEE::writeMask(const Mat &m, const QString &mask, const QString &targetSigset, const QString &querySigset)
-{
-    writeMatrix<Mask_t>(m, mask, targetSigset, querySigset);
-}
-
 void BEE::readMatrixHeader(const QString &matrix, QString *targetSigset, QString *querySigset)
 {
     qDebug("Reading %s header.", qPrintable(matrix));
@@ -235,8 +226,7 @@ void BEE::writeMatrixHeader(const QString &matrix, const QString &targetSigset, 
 {
     qDebug("Writing %s header to %s %s.", qPrintable(matrix), qPrintable(targetSigset), qPrintable(querySigset));
 
-    if (matrix.endsWith("mask")) writeMatrix<  Mask_t>(readMat(matrix), matrix, targetSigset, querySigset);
-    else                         writeMatrix<Simmat_t>(readMat(matrix), matrix, targetSigset, querySigset);
+    writeMat(readMat(matrix), matrix, targetSigset, querySigset);
 }
 
 void BEE::makeMask(const QString &targetInput, const QString &queryInput, const QString &mask)
@@ -245,11 +235,11 @@ void BEE::makeMask(const QString &targetInput, const QString &queryInput, const 
     FileList targets = TemplateList::fromGallery(targetInput).files();
     FileList queries = (queryInput == ".") ? targets : TemplateList::fromGallery(queryInput).files();
     int partitions = targets.first().get<int>("crossValidate");
-    if (partitions == 0) writeMask(makeMask(targets, queries), mask, targetInput, queryInput);
+    if (partitions == 0) writeMat(makeMask(targets, queries), mask, targetInput, queryInput);
     else {
         if (!mask.contains("%1")) qFatal("Mask file name missing partition number place marker (%%1)");
         for (int i=0; i<partitions; i++) {
-            writeMask(makeMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
+            writeMat(makeMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
         }
     }
 }
@@ -259,11 +249,11 @@ void BEE::makePairwiseMask(const QString &targetInput, const QString &queryInput
     FileList targets = TemplateList::fromGallery(targetInput).files();
     FileList queries = (queryInput == ".") ? targets : TemplateList::fromGallery(queryInput).files();
     int partitions = targets.first().get<int>("crossValidate");
-    if (partitions == 0) writeMask(makePairwiseMask(targets, queries), mask, targetInput, queryInput);
+    if (partitions == 0) writeMat(makePairwiseMask(targets, queries), mask, targetInput, queryInput);
     else {
         if (!mask.contains("%1")) qFatal("Mask file name missing partition number place marker (%%1)");
         for (int i=0; i<partitions; i++) {
-            writeMask(makePairwiseMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
+            writeMat(makePairwiseMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
         }
     }
 }
@@ -387,5 +377,5 @@ void BEE::combineMasks(const QStringList &inputMasks, const QString &outputMask,
         }
     }
 
-    writeMask(combinedMask, outputMask, "Combined_Targets", "Combined_Queries");
+    writeMat(combinedMask, outputMask, "Combined_Targets", "Combined_Queries");
 }
diff --git a/openbr/core/bee.h b/openbr/core/bee.h
index ba561db..313708a 100644
--- a/openbr/core/bee.h
+++ b/openbr/core/bee.h
@@ -40,8 +40,7 @@ namespace BEE
 
     // Matrix
     cv::Mat readMat(const br::File & mat, QString * targetSigset = NULL, QString * querySigset = NULL);
-    void writeSimmat(const cv::Mat &m, const QString &simmat, const QString &targetSigset = "Unknown_Target", const QString &querySigset = "Unknown_Query");
-    void writeMask(const cv::Mat &m, const QString &mask, const QString &targetSigset = "Unknown_Target", const QString &querySigset = "Unknown_Query");
+    void writeMat(const cv::Mat &m, const QString &simmat, const QString &targetSigset = "Unknown_Target", const QString &querySigset = "Unknown_Query");
     void readMatrixHeader(const QString &matrix, QString *targetSigset, QString *querySigset);
     void writeMatrixHeader(const QString &matrix, const QString &targetSigset, const QString &querySigset);
 
diff --git a/openbr/core/core.cpp b/openbr/core/core.cpp
index e2baab4..fae1184 100644
--- a/openbr/core/core.cpp
+++ b/openbr/core/core.cpp
@@ -235,15 +235,21 @@ struct AlgorithmCore
         TemplateList targets = t->read();
 
         // Use a single file for one of the dimensions so that the output makes the right size file
-        FileList dummyQuery;
-        dummyQuery.append(targets[0]);
-        QScopedPointer<Output> realOutput(Output::make(output, targetFiles, dummyQuery));
-
+        FileList dummyTarget;
+        dummyTarget.append(targets[0]);
+        QScopedPointer<Output> realOutput(Output::make(output, dummyTarget, queryFiles));
+
+        // Some outputs assume Globals->blockSize is a real thing, of course we have no interest in it.
+        int old_block_size = Globals->blockSize;
+        Globals->blockSize = INT_MAX;
+        realOutput->setBlock(0,0);
         for (int i=0; i < queries.length(); i++)
         {
             float res = distance->compare(queries[i], targets[i]);
             realOutput->setRelative(res, 0,i);
         }
+
+        Globals->blockSize = old_block_size;
     }
 
     void compare(File targetGallery, File queryGallery, File output)
diff --git a/openbr/core/fuse.cpp b/openbr/core/fuse.cpp
index 89306c3..f2a6e53 100644
--- a/openbr/core/fuse.cpp
+++ b/openbr/core/fuse.cpp
@@ -160,5 +160,5 @@ void br::Fuse(const QStringList &inputSimmats, const QString &normalization, con
 
     } while (partition < crossValidate);
 
-    BEE::writeSimmat(buffer, outputSimmat);
+    BEE::writeMat(buffer, outputSimmat);
 }
diff --git a/openbr/plugins/format.cpp b/openbr/plugins/format.cpp
index 258a06d..6e0800d 100644
--- a/openbr/plugins/format.cpp
+++ b/openbr/plugins/format.cpp
@@ -285,7 +285,7 @@ class mtxFormat : public Format
 
     void write(const Template &t) const
     {
-        BEE::writeSimmat(t, file);
+        BEE::writeMat(t, file);
     }
 };
 
@@ -307,7 +307,7 @@ class maskFormat : public Format
 
     void write(const Template &t) const
     {
-        BEE::writeMask(t, file);
+        BEE::writeMat(t, file);
     }
 };
 
@@ -418,9 +418,7 @@ class matFormat : public Format
                 }
 
                 if ((rows > 0) && (columns > 0) && (matrixType != 0) && !matrixData.isEmpty()) {
-                    Mat transposed;
-                    transpose(Mat(rows, columns, matrixType, matrixData.data()), transposed);
-                    t.append(transposed);
+                    t.append(Mat(rows, columns, matrixType, matrixData.data()));
                 }
             }
         }