.. _inspecting-your-results:

Inspecting the results of your analysis (Quality Control, FSLeyes)
##################################################################

.. _qc:

Quality Control (QC) Reports
****************************

SCT provides a web browser-based interface called a Quality Control (QC) Report. Each QC report contains a table of image entries. Clicking on an entry in the table will show a mosaic of slice images, as well as an overlay that can highlight cord segmentations, WM/GM tract volumes, and more.

How can I generate a QC report?
-------------------------------

To generate a QC report, check to see if the command you're using supports the ``-qc`` flag. For example:

.. code:: sh

    # Basic command (no QC)
    sct_propseg -i t2.nii.gz -c t2

    # Command with QC flag added
    sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_folder

Once you specify the ``-qc`` flag, a QC report will be automatically generated in whichever folder you specified. You can specify the same folder as many times as you like.

How do I open the QC report?
----------------------------

At the very bottom of the terminal output for your command, instructions will be printed to help you open the QC report:

.. code:: sh

   # Sample output (macOS) after running the SCT script
   Use the following command to see the results in a browser:
   open "qc_folder/index.html"

.. code:: sh

   # Sample output (Linux) after running the SCT script
   Use the following command to see the results in a browser:
   xdg-open "qc_folder/index.html"

If you already have the page open, and you run new commands, you can simply refresh the page to display new QC report entries.

How do I use the QC report?
---------------------------

Once you run the ``open`` command, the QC report page will open up in your web browser for you to interact with.

.. image:: https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/quality-control/qc.png
  :align: center
  :height: 400px

From the table on the left side, you can:

  * **Navigate between images** using the arrow keys or mouse.
  * **Toggle the overlay** using the right arrow key.
  * **Evaluate and mark images** using the ``f`` key. Pressing once marks the highlighted image as "Pass", twice marks it as "Fail", and three times marks it as "Artifact".
  * **Export the marked images** in a list format using the buttons at the bottom of the table.

This workflow is especially useful if you are performing multi-subject batch analyses, as QC reports allow you to quickly review many output files at once using your keyboard.

.. _fsleyes-instructions:

FSLeyes
*******

If you have the `FSLeyes <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes>`_ tool installed, then some of SCT's scripts will also print a ``fsleyes`` command as part of their output.

.. code:: sh

   # Sample output after running an SCT script
   Done! To view results, type:
   fsleyes t2/t2.nii.gz -cm greyscale t2/t2_seg.nii.gz -cm red -a 100.0 &

Running this command will display a viewer that you can interact with. For more information about how to use FSLeyes, visit the `FSLeyes documentation <https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/>`_.

.. image:: https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/quality-control/fsleyes.png
  :align: center
  :height: 400px