.. _CT_Reconstruction:

CT Reconstruction
==================

CT Reconstruction module computes a CT volume from a set of X-ray projections acquired in a calibrated geometry.
Any geometry misalignment may pose artifacts in the CT volume, reduce the contrast and quality of the reconstruction.
Therefore, it is recommended to calibrate the geometry prior to the CT reconstruction.

.. note:: Ensure projection geometry is correctly set up before reconstruction. See :ref:`CT Geometry <CT_Geometry>` for modern geometry configuration and visualization.

Once the projection data is loaded into the Imfusion Suite workspace, the CT Reconstruction algorithm can be openned from the associated algorithm menu of the projections. 

.. image:: img/recon_launch.png

Now, select the problem formulation from the ``Problem`` drop box in the CT Reconstruction controller.

.. image:: img/recon_prob.png

Once the problem is set, the ``Solver`` list will allow to select the corresponding solvers supported by the problem formulation.

.. image:: img/recon_solver.png

Then, depending on the problem and solver selections, extra algorithm configurations are needed. For example, **FDK** solver works with different ``Additional weighting`` schemes, while iterative solvers such as **SQS** requires ``maxIterations`` to be specified.  
  
.. image:: img/recon_config.png

Further adjustments can be made for the **OptiomizationProblem**.

Now, adjusting the **Volume Descriptor**:

.. image:: img/recon_vol_desc.png

**Volume Descriptor** allows to specify:

* ``type``: Data type of the reconstruction, can be seleted from the list.
* ``width``: Width of the CT volume in voxel. 
* ``height``: Height of the CT volume in voxel. 
* ``slices``: Number of slices in the CT volume. 
* ``spacing``: Space between centers of two neighboring voxels, in *mm*.
* ``center``: Coordinates of the volume center relative to the isocenter.

Upon adjusting the size of the CT volume, one can enable ``Show bounding boxes`` in the controller for the visualization of the volume bounding box in the 3D view, or directly adjust the bounding box from the slice view and the changes are updated in the 3D view.

.. image:: img/recon_boundingbox.png

After all necessary configurations are done, we can now start the reconstruction process by clicking the ``Compute`` button at the bottom of the controller.

.. image:: img/recon_compute.png

The reconstruction will be updated and a progress bar will be displaying the current status of the computation.

.. image:: img/recon_volume.png

Once it is done, the reconstructed slices and the CT volume can be viewed from the slice and 3D view of Imfusion Suite. 


Additional parameters
---------------------
- **regionOfInterestEnabled** (bool): Enables ROI reconstruction with an additional outer bounding box that can be edited in the 3D view.
- **shiftAndScale** (vec2): Calibrated intensity shift and scale applied to the input projections during reconstruction.