Stage 4: Intermediate processing


Stage summary: Intermediate automatic processing

  1. Second inhomogeneity correction using N4
  2. Generation of grey matter, white matter and CSF tissue segmentation
  3. Generation of ACPC T1 and ACPC T1 erode

ITK-SNAP keyboard shortcuts

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


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.