diff --git a/doxygen/doxygengroups.h b/doxygen/doxygengroups.h
new file mode 100644
index 000000000..ece254fed
--- /dev/null
+++ b/doxygen/doxygengroups.h
@@ -0,0 +1,55 @@
+/*
+CCP PETMR Synergistic Image Reconstruction Framework (SIRF)
+Copyright 2019 University College London
+
+This is software developed for the Collaborative Computational
+Project in Positron Emission Tomography and Magnetic Resonance imaging
+(http://www.ccppetmr.ac.uk/).
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+*/
+
+// define some doxygen groups and namespace
+// This file does not contain any code
+
+/*! \namespace sirf
+  \brief Namespace for the SIRF library (and some/most of its applications)
+
+  This namespace encompasses the whole
+  library. All classes, functions and symbols are in this namespace.
+  This has the effect that conflicts with any other library is
+  impossible (except if that library uses the same namespace...).
+*/
+
+/*!
+\defgroup PET SIRF PET
+\ingroup SIRF
+All PET functionality of SIRF.
+*/
+
+/*!
+\defgroup MR SIRF MR
+\ingroup SIRF
+All MR functionality of SIRF.
+*/
+
+/*!
+\defgroup Registration SIRF registration
+\ingroup SIRF
+All registration/resampling functionality of SIRF.
+*/
+
+/*!
+\defgroup Synergistic SIRF synergistic
+\ingroup SIRF
+All synergistic functionality of SIRF.
+*/
diff --git a/src/Registration/cReg/NiftiImageData3D.cpp b/src/Registration/cReg/NiftiImageData3D.cpp
index 5ae6f5454..b47a6ed63 100644
--- a/src/Registration/cReg/NiftiImageData3D.cpp
+++ b/src/Registration/cReg/NiftiImageData3D.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for SIRF image data.
+\brief Base class for 3D SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Registration/cReg/NiftiImageData3DTensor.cpp b/src/Registration/cReg/NiftiImageData3DTensor.cpp
index 46be27ac4..58fdd1e72 100644
--- a/src/Registration/cReg/NiftiImageData3DTensor.cpp
+++ b/src/Registration/cReg/NiftiImageData3DTensor.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation and displacement SIRF image data.
+\brief Class for tensor SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Registration/cReg/NiftyRegistration.cpp b/src/Registration/cReg/NiftyRegistration.cpp
index 85a8c8295..85a9401dd 100644
--- a/src/Registration/cReg/NiftyRegistration.cpp
+++ b/src/Registration/cReg/NiftyRegistration.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for all SIRF registration.
+\brief Base class for all NiftyReg registration algorithms.
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Registration/cReg/Resample.cpp b/src/Registration/cReg/Resample.cpp
index 8f14ef619..bb95513e1 100644
--- a/src/Registration/cReg/Resample.cpp
+++ b/src/Registration/cReg/Resample.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief bstract resampling base class
+\brief Abstract resampling base class
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Registration/cReg/include/sirf/cReg/AffineTransformation.h b/src/Registration/cReg/include/sirf/cReg/AffineTransformation.h
index 62e6708dc..dd3878b8e 100644
--- a/src/Registration/cReg/include/sirf/cReg/AffineTransformation.h
+++ b/src/Registration/cReg/include/sirf/cReg/AffineTransformation.h
@@ -33,7 +33,12 @@ limitations under the License.
 #include "sirf/cReg/Transformation.h"
 
 namespace sirf {
-///Class for affine transformations
+/*!
+\ingroup Registration
+\brief Class for affine transformations.
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class AffineTransformation : public Transformation<dataType>
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/ImageWeightedMean.h b/src/Registration/cReg/include/sirf/cReg/ImageWeightedMean.h
index dcd4bc11f..439147465 100644
--- a/src/Registration/cReg/include/sirf/cReg/ImageWeightedMean.h
+++ b/src/Registration/cReg/include/sirf/cReg/ImageWeightedMean.h
@@ -37,7 +37,16 @@ namespace sirf {
 // Forward delcarations
 template<class dataType> class NiftiImageData;
 
-/// Calculate the weighted mean of a set of images
+/*!
+\file
+\ingroup Registration
+\brief Perform weighted mean of multiple images.
+
+TODO - would be simple for this to work in terms of ImageData instead of NiftiImageData.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class ImageWeightedMean
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftiImageData.h b/src/Registration/cReg/include/sirf/cReg/NiftiImageData.h
index 27cb45f04..6be5b2d10 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftiImageData.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftiImageData.h
@@ -23,22 +23,6 @@ limitations under the License.
 \ingroup Registration
 \brief Base class for SIRF nifti image data.
 
-Generally SIRF (not necessarily NiftyReg) will preferentially use
-the qform over the sform code. This is the same for ITK and ANTs, but
-is not the case for SPM/MRIcroGL/FSLeyes/Mango.
-
-qform/sform
-The qform code describes "scanner-anatomical" coordinates, whereas the
-sform code describes the location of the voxels in some standard space.
-
-For qform > 0, the origin of coordinates would generally be whatever
-the scanner origin is; for example, in MRI, (0,0,0) is the center
-of the gradient coil.
-
-For sform > 0, the origin of coordinates would depend on the value
-of sform_code; for example, for the Talairach coordinate system,
-(0,0,0) corresponds to the Anterior Commissure.
-
 \author Richard Brown
 \author CCP PETMR
 */
@@ -57,7 +41,37 @@ of sform_code; for example, for the Talairach coordinate system,
 
 namespace sirf {
 
-/// SIRF image data
+/*!
+\file
+\ingroup Registration
+\brief Base class for SIRF's nifti image data.
+
+This is a wrapper around the basic nifti_image (stored as a sptr),
+with extra functionality.
+
+This is the general form, and any number of dimensions are allowed. 
+This is contrary to the derived classes, which have specific requirements
+(e.g., NiftiImageData3DDeformation requires 5 dimensions, of which the 4th (time) == 1).
+
+To move between different images types (e.g., STIRImageData and MRImageData), 
+we need to know the patient's position relative to the scanner. For this, only
+qform_code == 1 will suffice.
+
+qform/sform
+The qform code describes "scanner-anatomical" coordinates, whereas the
+sform code describes the location of the voxels in some standard space.
+
+For qform > 0, the origin of coordinates would generally be whatever
+the scanner origin is; for example, in MRI, (0,0,0) is the center
+of the gradient coil.
+
+For sform > 0, the origin of coordinates would depend on the value
+of sform_code; for example, for the Talairach coordinate system,
+(0,0,0) corresponds to the Anterior Commissure.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData : public ImageData
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3D.h b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3D.h
index 206c44682..783b76b78 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3D.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3D.h
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for SIRF image data.
+\brief 3D Nifti image.
 
 \author Richard Brown
 \author CCP PETMR
@@ -33,7 +33,15 @@ limitations under the License.
 
 namespace sirf {
 
-/// SIRF image data
+/*!
+\ingroup Registration
+\brief 3D Nifti image.
+
+Here, we require that the number of dimensions == 3.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3D : public NiftiImageData<dataType>
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDeformation.h b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDeformation.h
index 9c5c4e9c3..7fec37215 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDeformation.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDeformation.h
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation/displacement SIRF image data.
+\brief Class for deformation SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
@@ -38,7 +38,16 @@ namespace sirf {
 template<class dataType> class NiftiImageData3D;
 template<class dataType> class NiftiImageData3DDisplacement;
 
-/// SIRF nifti image data deformation field image
+/*!
+\ingroup Registration
+\brief Class for deformation SIRF image data.
+
+Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u==3 for the tensor component).
+Also require intent_p1 == DEF_FIELD.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3DDeformation : public NiftiImageData3DTensor<dataType>, public Transformation<dataType>
 {
@@ -68,7 +77,7 @@ class NiftiImageData3DDeformation : public NiftiImageData3DTensor<dataType>, pub
     /// Create from 3D image
     void create_from_3D_image(const NiftiImageData3D<dataType> &image);
 
-    /// Create from CPP image
+    /// Create from control point grid image
     void create_from_cpp(NiftiImageData3DTensor<dataType> &cpp, const NiftiImageData3D<dataType> &ref);
 
     /// Get as deformation field
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDisplacement.h b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDisplacement.h
index b374ecff2..fe02e0b61 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDisplacement.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDisplacement.h
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation/displacement SIRF image data.
+\brief Class for displacement SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
@@ -36,7 +36,16 @@ limitations under the License.
 namespace sirf {
 template<class dataType> class NiftiImageData3D;
 
-/// SIRF nifti image data displacement field image
+/*!
+\ingroup Registration
+\brief Class for displacement SIRF image data.
+
+Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u==3 for the tensor component).
+Also require intent_p1 == DISP_FIELD.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3DDisplacement : public NiftiImageData3DTensor<dataType>, public Transformation<dataType>
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DTensor.h b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DTensor.h
index ece99a69d..592636baf 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DTensor.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftiImageData3DTensor.h
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation/displacement SIRF image data.
+\brief Class for tensor SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
@@ -36,7 +36,17 @@ namespace sirf {
 // Forward declarations
 template<class dataType> class NiftiImageData3D;
 
-/// SIRF image data
+/*!
+\ingroup Registration
+\brief Class for tensor SIRF image data.
+
+Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u==3 for the tensor component).
+This is the general tensor class, so we do not care if the image is a deformation or displacement field (or any other type).
+Hence, any value of intent_p1 is fine.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3DTensor : public NiftiImageData<dataType>
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftyAladinSym.h b/src/Registration/cReg/include/sirf/cReg/NiftyAladinSym.h
index cf9dc47a9..855dfb9d5 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftyAladinSym.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftyAladinSym.h
@@ -38,7 +38,15 @@ namespace sirf {
 /// Forward declarations
 template<class dataType> class AffineTransformation;
 
-/// Wrapper around NiftyReg's aladin class for rigid and affine transformations
+/*!
+\ingroup Registration
+\brief NiftyReg's aladin class for rigid and affine registrations.
+
+Since this algorithm is affine/rigid, it can also return a transformation matrix if desired.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType> class NiftyAladinSym : public NiftyRegistration<dataType>
 {
 public:
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftyF3dSym.h b/src/Registration/cReg/include/sirf/cReg/NiftyF3dSym.h
index 6d1a01ed6..aacb946ff 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftyF3dSym.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftyF3dSym.h
@@ -38,7 +38,18 @@ namespace sirf {
 /// Forward declarations
 template<class dataType> class AffineTransformation;
 
-/// Wrapper around NiftyReg's f3d class for non-rigid transformations
+/*!
+\ingroup Registration
+\brief NiftyReg's f3d class for non-rigid registrations.
+
+User can set an initial affine transformation if desired. 
+
+In theory, multiple time points can be used, but thus far has only been tested for
+t == 1 for both reference and floating images.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType> class NiftyF3dSym : public NiftyRegistration<dataType>
 {
 public:
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftyRegistration.h b/src/Registration/cReg/include/sirf/cReg/NiftyRegistration.h
index fd323bf88..7ae1a8fa8 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftyRegistration.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftyRegistration.h
@@ -21,24 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for all SIRF registration.
-
-The parameter file should have interfile-like syntax.
-The variables will be stored as a vector of floats and converted into the required type (int, unsigned int, etc) if necessary.
-Multiple variables for a given parameter should be comma separated.
-Spaces and tabs will be ignored.
-For the title, it doesn't matter what is written as it will be ignored, but something has to be there (otherwise the first parameter will be ignored).
-Possible parameters are all the Set<something> methods for each class (e.g., nifty_aladin::SetPerformRigid) and should be written in the parameter file without the "Set" (e.g., PerformRigid).
-
-An example is given below:
-    SomeTitle :=
-        ReferenceTimePoint := 1
-        FloatingTimePoint := 2
-        LinearEnergyWeights := 1.5,1
-        AdditiveMC :=
-    end :=
-
-More examples can be found in data/examples/Registration/paramFiles
+\brief Base class for all NiftyReg registrations.
 
 \author Richard Brown
 \author CCP PETMR
@@ -53,7 +36,13 @@ namespace sirf {
 /// Forward declarations
 template<class dataType> class NiftiImageData3D;
 
-/// Base class for wrapped NiftyReg registration algorithms
+/*!
+\ingroup Registration
+\brief Base class for all NiftyReg registrations.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftyRegistration : public Registration<dataType>
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/NiftyResample.h b/src/Registration/cReg/include/sirf/cReg/NiftyResample.h
index 2f578b2c6..7e6fbde7b 100644
--- a/src/Registration/cReg/include/sirf/cReg/NiftyResample.h
+++ b/src/Registration/cReg/include/sirf/cReg/NiftyResample.h
@@ -23,12 +23,6 @@ limitations under the License.
 \ingroup Registration
 \brief Resampling class based on nifty resample
 
-If multiple transformations are set, they will be used in the order that they have been added.
-i.e., Trans3(Trans2(Trans1(x))).
-
-The reference image must be 3D (i.e., NiftiImageData3D), but the floating image (and therefore
-the output image) can have nt and/or nu != 1.
-
 \author Richard Brown
 \author CCP PETMR
 */
@@ -50,7 +44,16 @@ namespace sirf {
 template<class dataType> class NiftiImageData3DDisplacement;
 template<class dataType> class AffineTransformation;
 
-/// Wrapper around NiftyReg's resample class
+/*!
+\ingroup Registration
+\brief Resampling class based on nifty resample
+
+The reference image must be 3D (i.e., NiftiImageData3D), but the floating image (and therefore
+the output image) can have nt and/or nu != 1.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftyResample : public Resample<dataType>
 {
@@ -76,11 +79,11 @@ class NiftyResample : public Resample<dataType>
     /// Set up the output image
     void set_up_output_image();
 
-    /// Reference image as a NiftyImageData3D
+    /// Reference image as a NiftiImageData3D
     std::shared_ptr<const NiftiImageData3D<dataType> > _reference_image_nifti_sptr;
-    /// Floating image as a NiftyImageData
+    /// Floating image as a NiftiImageData
     std::shared_ptr<const NiftiImageData<dataType> > _floating_image_nifti_sptr;
-    /// Floating image as a NiftyImageData
+    /// Floating image as a NiftiImageData
     std::shared_ptr<NiftiImageData<dataType> >       _output_image_nifti_sptr;
 };
 }
diff --git a/src/Registration/cReg/include/sirf/cReg/Parser.h b/src/Registration/cReg/include/sirf/cReg/Parser.h
index bb7446fa5..c80cf6ec9 100644
--- a/src/Registration/cReg/include/sirf/cReg/Parser.h
+++ b/src/Registration/cReg/include/sirf/cReg/Parser.h
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief NiftyReg's aladin class for rigid and affine registrations.
+\brief Small class to parse parameter files.
 
 \author Richard Brown
 \author CCP PETMR
@@ -37,7 +37,14 @@ limitations under the License.
 #include <type_traits>
 
 namespace sirf {
-/// Reg parser
+/*!
+\file
+\ingroup Registration
+\brief Small class to parse parameter files.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class Z>
 class Parser
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/ParserKey.h b/src/Registration/cReg/include/sirf/cReg/ParserKey.h
index f459e1694..ab365c532 100644
--- a/src/Registration/cReg/include/sirf/cReg/ParserKey.h
+++ b/src/Registration/cReg/include/sirf/cReg/ParserKey.h
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief NiftyReg's aladin class for rigid and affine registrations.
+\brief Parser keys for 0, 1 and 2 arguments
 
 \author Richard Brown
 \author CCP PETMR
@@ -47,7 +47,13 @@ std::string get_typeid(A)
     else                                         return "unknown";
 }
 
-/// Abstract base class for a parser key
+/*!
+\ingroup Registration
+\brief Base for parser keys
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class Z>
 class ParserKeyBase
 {
@@ -140,7 +146,13 @@ class ParserKeyBase
     std::shared_ptr<Z> _object;
 };
 
-/// Abstract base class for a parser key with 0 arguments
+/*!
+\ingroup Registration
+\brief Class for parser keys with 0 arguments
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class Z>
 class ParserKey0Arg : public ParserKeyBase<Z>
 {
@@ -173,7 +185,13 @@ class ParserKey0Arg : public ParserKeyBase<Z>
     void (Z::*_function)();
 };
 
-/// Abstract base class for a parser key with 1 argument
+/*!
+\ingroup Registration
+\brief Class for parser keys with 1 argument
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class Z, class A>
 class ParserKey1Arg : public ParserKeyBase<Z>
 {
@@ -213,7 +231,13 @@ class ParserKey1Arg : public ParserKeyBase<Z>
     A _arg1;
 };
 
-/// Abstract base class for a parser key with 2 arguments
+/*!
+\ingroup Registration
+\brief Class for parser keys with 2 arguments
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class Z, class A, class B>
 class ParserKey2Arg : public ParserKeyBase<Z>
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/Registration.h b/src/Registration/cReg/include/sirf/cReg/Registration.h
index 2c848a38c..1f04b996f 100644
--- a/src/Registration/cReg/include/sirf/cReg/Registration.h
+++ b/src/Registration/cReg/include/sirf/cReg/Registration.h
@@ -23,7 +23,29 @@ limitations under the License.
 \ingroup Registration
 \brief Base class for all SIRF registration.
 
-The parameter file should have interfile-like syntax.
+\author Richard Brown
+\author CCP PETMR
+*/
+
+#pragma once
+
+#include <string>
+#include <vector>
+#include <memory>
+
+namespace sirf {
+
+/// Forward declarations
+template<class dataType> class Transformation;
+class ImageData;
+
+/*!
+\ingroup Registration
+\brief Base class for all SIRF registration.
+
+Registration classes can be set up with parameter files or inputting arguments directly with the set_parameter() method.
+
+If using a parameter file, it should have interfile-like syntax.
 The variables will be stored as a vector of floats and converted into the required type (int, unsigned int, etc) if necessary.
 Multiple variables for a given parameter should be comma separated.
 Spaces and tabs will be ignored.
@@ -31,32 +53,20 @@ For the title, it doesn't matter what is written as it will be ignored, but some
 Possible parameters are all the Set<something> methods for each class (e.g., nifty_aladin::SetPerformRigid) and should be written in the parameter file without the "Set" (e.g., PerformRigid).
 
 An example is given below:
+\verbatim
     SomeTitle :=
         ReferenceTimePoint := 1
         FloatingTimePoint := 2
         LinearEnergyWeights := 1.5,1
         AdditiveMC :=
     end :=
+\endverbatim
 
 More examples can be found in data/examples/Registration/paramFiles
 
 \author Richard Brown
 \author CCP PETMR
 */
-
-#pragma once
-
-#include <string>
-#include <vector>
-#include <memory>
-
-namespace sirf {
-
-/// Forward declarations
-template<class dataType> class Transformation;
-class ImageData;
-
-/// Base class for SIRF registration algorithms
 template<class dataType>
 class Registration
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/Resample.h b/src/Registration/cReg/include/sirf/cReg/Resample.h
index 26a6b5ec9..28c8ea12f 100644
--- a/src/Registration/cReg/include/sirf/cReg/Resample.h
+++ b/src/Registration/cReg/include/sirf/cReg/Resample.h
@@ -23,9 +23,6 @@ limitations under the License.
 \ingroup Registration
 \brief Abstract resampling base class
 
-If multiple transformations are set, they will be used in the order that they have been added.
-i.e., Trans3(Trans2(Trans1(x))).
-
 \author Richard Brown
 \author CCP PETMR
 */
@@ -41,7 +38,17 @@ namespace sirf {
 template<class dataType> class Transformation;
 class ImageData;
 
-/// Wrapper around NiftyReg's resample class
+/*!
+\file
+\ingroup Registration
+\brief Abstract resampling base class
+
+If multiple transformations are set, they will be used in the order that they have been added.
+i.e., Trans3(Trans2(Trans1(x))).
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class Resample
 {
diff --git a/src/Registration/cReg/include/sirf/cReg/Transformation.h b/src/Registration/cReg/include/sirf/cReg/Transformation.h
index b3b0efa3c..0cf85d392 100644
--- a/src/Registration/cReg/include/sirf/cReg/Transformation.h
+++ b/src/Registration/cReg/include/sirf/cReg/Transformation.h
@@ -36,8 +36,17 @@ namespace sirf {
 template<class dataType> class NiftiImageData3D;
 template<class dataType> class NiftiImageData3DDeformation;
 
-/// Base class for transformations
-template<class dataType>
+/*!
+\ingroup Registration
+\brief Base class for transformations.
+
+All transformations need to be able to convert themselves
+to a deformation field. In this fashion, they can be composed
+into a single transformation.
+
+\author Richard Brown
+\author CCP PETMR
+*/template<class dataType>
 class Transformation
 {
 public:
diff --git a/src/Registration/cReg/sirf_change_datatype.cpp b/src/Registration/cReg/sirf_change_datatype.cpp
index 7f334b876..cb507e2df 100644
--- a/src/Registration/cReg/sirf_change_datatype.cpp
+++ b/src/Registration/cReg/sirf_change_datatype.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Convert affine transformation matrix to displacement or deformation field image(s)
+\brief Change the datatype of a nifti image (e.g., int->float)
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Registration/cReg/sirf_crop_image.cpp b/src/Registration/cReg/sirf_crop_image.cpp
index bc6fb1eb0..7a6846d6a 100644
--- a/src/Registration/cReg/sirf_crop_image.cpp
+++ b/src/Registration/cReg/sirf_crop_image.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Convert affine transformation matrix to displacement or deformation field image(s)
+\brief Crop a nifti image
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Registration/cReg/sirf_print_nifti_info.cpp b/src/Registration/cReg/sirf_print_nifti_info.cpp
index 91632a429..9ef87bcbd 100644
--- a/src/Registration/cReg/sirf_print_nifti_info.cpp
+++ b/src/Registration/cReg/sirf_print_nifti_info.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Dump info of a nifti image
+\brief Dump info of one or more nifti images
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Registration/mReg/+mReg/NiftiImageData3D.m b/src/Registration/mReg/+mReg/NiftiImageData3D.m
index 26653fda8..5936f5021 100644
--- a/src/Registration/mReg/+mReg/NiftiImageData3D.m
+++ b/src/Registration/mReg/+mReg/NiftiImageData3D.m
@@ -1,5 +1,5 @@
 classdef NiftiImageData3D < mReg.NiftiImageData
-% Class for image data.
+% Class for 3D image data.
 
 % CCP PETMR Synergistic Image Reconstruction Framework (SIRF).
 % Copyright 2018-2019 University College London
diff --git a/src/Registration/mReg/+mReg/NiftyResample.m b/src/Registration/mReg/+mReg/NiftyResample.m
index 37098ad61..57d56e6f4 100644
--- a/src/Registration/mReg/+mReg/NiftyResample.m
+++ b/src/Registration/mReg/+mReg/NiftyResample.m
@@ -1,5 +1,5 @@
 classdef NiftyResample < handle
-% Class resampling nifti image using NiftyReg.
+% Class for resampling using NiftyReg.
 
 % CCP PETMR Synergistic Image Reconstruction Framework (SIRF).
 % Copyright 2018-2019 University College London
diff --git a/src/Registration/pReg/Reg.py b/src/Registration/pReg/Reg.py
index c3b636052..4804f94b4 100644
--- a/src/Registration/pReg/Reg.py
+++ b/src/Registration/pReg/Reg.py
@@ -218,7 +218,7 @@ def get_as_deformation_field(self, ref):
 
 class NiftiImageData(SIRF.ImageData):
     """
-    General class for nifti image.
+    General class for nifti image data.
     """
     def __init__(self, src=None):
         self.handle = None
@@ -391,9 +391,15 @@ def print_headers(to_print):
             raise error('print_headers only implemented for up to 5 images.')
 
 
+class ImageData(NiftiImageData):
+    """
+    Alias class for nifti image data.
+    """
+
+
 class NiftiImageData3D(NiftiImageData):
     """
-    3D nifti image.
+    Class for 3D nifti image data.
     """
     def __init__(self, src=None):
         self.handle = None
@@ -424,15 +430,9 @@ def copy_data_to(self, pet_image):
         try_calling(pyreg.cReg_NiftiImageData3D_copy_data_to(self.handle, pet_image.handle))
 
 
-class ImageData(NiftiImageData3D):
-    """
-    3D nifti image.
-    """
-
-
 class NiftiImageData3DTensor(NiftiImageData):
     """
-    3D tensor nifti image.
+    Class for 3D tensor nifti image data.
     """
     def __init__(self, src1=None, src2=None, src3=None):
         self.handle = None
@@ -480,7 +480,7 @@ def flip_component(self, dim):
 
 class NiftiImageData3DDisplacement(NiftiImageData3DTensor, _Transformation):
     """
-    3D tensor displacement nifti image.
+    Class for 3D displacement nifti image data.
     """
     def __init__(self, src1=None, src2=None, src3=None):
         self.handle = None
@@ -505,7 +505,7 @@ def __del__(self):
 
 class NiftiImageData3DDeformation(NiftiImageData3DTensor, _Transformation):
     """
-    3D tensor deformation nifti image.
+    Class for 3D deformation nifti image data.
     """
 
     def __init__(self, src1=None, src2=None, src3=None):
diff --git a/src/Synergistic/sirf_do_images_match.cpp b/src/Synergistic/sirf_do_images_match.cpp
index dc19b033f..b15d077fa 100644
--- a/src/Synergistic/sirf_do_images_match.cpp
+++ b/src/Synergistic/sirf_do_images_match.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Check if two images match to a given precision.
+\brief Check if two SIRF images match to a given precision.
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Synergistic/sirf_registration.cpp b/src/Synergistic/sirf_registration.cpp
index f9a0c2cb5..96cbdaa0e 100644
--- a/src/Synergistic/sirf_registration.cpp
+++ b/src/Synergistic/sirf_registration.cpp
@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Perform registration with any type of SIRF image and any SIRF registration algorithm
+\brief Perform registration with any types of SIRF image and any SIRF registration algorithm.
 
 \author Richard Brown
 \author CCP PETMR
diff --git a/src/Synergistic/sirf_resample.cpp b/src/Synergistic/sirf_resample.cpp
index c74867913..b52f5aef0 100644
--- a/src/Synergistic/sirf_resample.cpp
+++ b/src/Synergistic/sirf_resample.cpp
@@ -22,6 +22,7 @@ limitations under the License.
 \file
 \ingroup Registration
 \brief Perform resampling with any type of SIRF image and any SIRF resampling algorithm.
+
 If no transformations are given, identity will be used.
 If multiple transformations are given, they will be applied in the order they were given.