Stage 1: Preprocessing

Files and parameters

Input files

Filename	Description
{session}_T1	T1 MRI
{session}_PD	PD MRI
{session}_T2	T2 MRI
{session}_FL	FLAIR MRI (optional)

Parameters

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

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

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