For using this package, you will need a DWI dicom data and skull stripped anatomical images ( if required). 
Command line parameters can be viewed by ./Executable_name -h

1. For converting the DWI dicom data to nrrd format use the executable "DicomToNrrdConverter". 
  example: ./DicomToNrrdConverter --inputDicomDirectory PATH --outputVolume PATH/DTI.nhdr
2. If you are carrying out registration between DWI- BO and anatomical data, make sure that they r oriented in the same manner. Check the direction cosines. 
   - If u want to use the 4D DTI image directly, use the DTIRigidRegistration, DTIAffineRegistration, DTIBSplineRegistration. These registration programs extract the B0 image and
   then use it. Therefore the movingImage will be the DTI.nhdr from step 1.
   example ./DTIAffineRegistration --fixedVolume T1.nrrd --movingVolume DTI.nhdr --outputVolume PATH/name.nrrd --outputTransform PATH/name.xfm 
3. For registration between 2 3D images, GeneralAffineRegistration,GeneralRigidRegistration and GeneralBsplineRegistration can be used. 
4. The deformation field can be obtained from ./TransformToDeformation. The size of the deformation field is based upon the reference input image ( usually the fixed image used
in the registration).
5../ComputeTensor computes the tensor image from DWI data ( nrrd format).
6. itkGradientRotate and itkGradientRotatePPD use the DWI data ( in nrrd format) , any kind of deformation field. It gives out reoriented tensor image. 
7. TensorReorient and TensorReorientPPD use the original tensor data and deformation field as inputs. Gives out the rotated tensors. 
8. DemonsRegistration executable performs Diffeomorphic demons registration, using histogram matching and a mean square metric. 
9. ComputeFA, Tensor_subtract can be used for analysis. 

