Stage 1: Preprocessing
======================

+----------------------+---------------------------------------------------------------------------------------------+
|.. image:: stage1.png | **Stage summary:** Preprocessing                                                            |
|                      |                                                                                             | 
|                      | #. Inhomogeneity correction using IHC                                                        |
|                      | #. Coregistering sequences to T1 acquisition space                                          |
|                      | #. Automatic removal of the brain and subdural CSF from the skull and surrounding tissue    |
|                      | #. Automatic generation of the T1-to-ACPC rotation matrix                                   |
+----------------------+---------------------------------------------------------------------------------------------+

Files and parameters
--------------------
Input files
^^^^^^^^^^^
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   * - Filename
     - Description
   * - ``{session}_T1``
     - T1 MRI
   * - ``{session}_PD``
     - PD MRI
   * - ``{session}_T2``
     - T2 MRI
   * - ``{session}_FL``
     - FLAIR MRI (optional)

Parameters
^^^^^^^^^^

.. list-table::
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   * - Parameter
     - Description
   * - Coregistration threshold
     - ``-t1t 0.X -t2t 0.X -pdt 0.X -flt 0.X``
   * - bet threshold
     - ``-f 0.X``
   * - TIV-E threshold
     - ``-p 0.X -t2t 0.X -t2reg``


Output files
^^^^^^^^^^^^
.. list-table::
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   * - Filename
     - Description
   * - ``{session}_T1_IHCpre``
     - T1 MRI corrected for inhomogeneity using N4 (intermediate file)
   * - ``{session}_PD_IHCpre``
     - PD MRI corrected for inhomogeneity using N4 (intermediate file)
   * - ``{session}_T2_IHCpre``
     - T2 MRI corrected for inhomogeneity using N4 (intermediate file)
   * - ``{session}_FL_IHCpre``
     - FLAIR MRI corrected for inhomogeneity using N4 (intermediate file)
   * - ``{session}_PD_IHCpre_inT1``
     - PD MRI coregistered and resliced to T1 acquisition space 
   * - ``{session}_T2_IHCpre_inT1``
     - T2 MRI coregistered and resliced to T1 acquisition space 
   * - ``{session}_FL_IHCpre_inT1``
     - FLAIR MRI coregistered and resliced to T1 acquisition space 
   * - ``{session}_TIVauto``   
     - Total Intracranial Volume Extraction (TIV-E) mask
   * - ``{session}_T1_IHCpre_iso``   
     - Isotropic T1
   * - ``{session}_T1_IHCpre_iso_086``   
     - Isotropic T1 with a forced 0.86 voxel size 
   * - ``{session}_T1_IHCpre_toACPC.mat``
     - T1-to-ACPC rotation matrix   

     
Quality check
-------------
.. list-table::
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   * - Filename
     - Description
   * - ``{session}_*_inT1``
     - Check coregistration by comparing the resliced images to the T1
   * - ``{session}_TIVauto``
     - Check TIV mask and manually fix under and over erosions using instructions found in Stage 2
   * - ``{session}_T1_IHCpre_toACPC.mat``
     - Check to ensure that ACPC matrix accurately rotates the T1 into ACPC space using instructions found in Stage 3