Using binary masks to compute CSA for gray and white matter
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First, we will use the gray and white matter segmentations to compute the cross sectional area of GM and WM. This is achieved using ``sct_process_segmentation``.

.. important:: There is a limit to the precision you can achieve for a given image resolution. SCT does not truncate spurious digits when performing angle correction, so please keep in mind that there may be non-significant digits in the computed values. You may wish to compare angle-corrected values with their corresponding uncorrected values to get a sense of the limits on precision.

Compute CSA
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.. code::

   sct_process_segmentation -i t2s_wmseg.nii.gz -o csa_wm.csv -perslice 1 -angle-corr 0

.. code::

   sct_process_segmentation -i t2s_gmseg.nii.gz -o csa_gm.csv -perslice 1 -angle-corr 0

:Input arguments:
   - ``-i`` : The input segmentation file.
   - ``-o`` : The output CSV file.
   - ``-perslice`` : Set this option to 1 to turn on per-slice computation.
   - ``-angle-corr 0``: Normally, angle correction will be applied during ``sct_process_segmentation`` to account for scans where the spinal cord is positioned at an angle with respect to the superior-inferior axis. While this works well when the input is a full spinal cord segmentation, in this case we are instead providing GM/WM segmentations only. The shape of these segmentations can have a negative effect on so the estimation of the cord centerline, which in turn may cause the estimated angle to be incorrect. So, here we specify ``0`` to turn off angle correction.
   - **Note:** Turning off angle correction is only safe to do if you know that your axial slices were acquired roughly orthogonal to the cord.


:Output files/folders:
   - ``csa_wm.csv`` and ``csa_gm.csv``: Two CSV files containing shape metrics for both the white and gray matter segmentations.

.. figure:: https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/gm-wm-metric-computation/io-sct_process_segmentation.png
   :align: center