Stage 4: Intermediate processing

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

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Files and parameters

Input files

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

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

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.