Stage 4: Intermediate processing ================ +----------------------+---------------------------------------------------------------------------------------------+ |.. image:: stage4.png | **Stage summary:** Intermediate automatic processing | | | | | | #. Second inhomogeneity correction using N4 | | | #. Generation of grey matter, white matter and CSF tissue segmentation | | | #. Generation of ACPC T1 and ACPC T1 erode | +----------------------+---------------------------------------------------------------------------------------------+ `ITK-SNAP keyboard shortcuts `_ Files and parameters -------------------- Input files ^^^^^^^^^^^ .. list-table:: :widths: 30, 70 :header-rows: 1 * - Filename - Description * - ``{session}_T1`` - T1 MRI * - ``{session}_TIVedit`` - Total Intracranial Volume Extraction (TIV-E) mask with manual intervention * - ``{session}_T1_IHCpre_iso`` - Isotropic T1 * - ``{session}_T1_IHCpre_toACPC.mat`` - T1-to-ACPC rotation matrix Parameters ^^^^^^^^^^ Output files ^^^^^^^^^^^^ .. list-table:: :widths: 30, 70 :header-rows: 1 * - Filename - Description * - ``{session}_T1_toACPC.air`` - T1-to-ACPC rotation matrix * - ``{session}_ACPC_toT1.air`` - ACPC-to-T1 rotation matrix * - ``{session}_T1_IHC`` - T1 MRI with a second N4 inhomogeneity correction * - ``{session}_T1_IHC_masked`` - Inhomogeneity corrected T1 MRI with skull and non-brain tissue masked out * - ``{session}_seg`` - Tissue segmentation mask * - ``{session}_T1_IHC_inACPC`` - T1 MRI aligned to the plane defined by the anterior and posterior commissure and resliced to isotropic voxels * - ``{session}_T1_IHC_erode_inACPC`` - 3D eroded T1 MRI in ACPC space * - ``{session}_T1_IHC_erode`` - 3D eroded T1 MRI in T1 acquisition space Quality check -------------- .. list-table:: :widths: 30, 70 :header-rows: 1 * - Filename - Description * - ``{session}_seg`` - Check that the grey and white matter have been properly segmented. Misclassification may occur with poor scan quality and/or T1 artifact. Ventricular CSF (vCSF) will be manually reassigned in Stage 6.