Check	Select operations you want to perform	Requires
	Reorient to radiological convention	T1 Anatomical File + (Optional: Lesion Mask File) Orientation
	Registration	T1 Anatomical File + (Optional: Lesion Mask File) Registration Method
	Brain Extraction	T1 Anatomical File + (Optional: Lesion Mask File) Brain Extraction Method
	White Matter Segmentation	T1 Anatomical File
	Lesion correction for white matter voxels	T1 Anatomical File + Lesion Mask File
	Lesion load calculation	T1 Anatomical File + Lesion Mask File
	Lesion heatmap	T1 Anatomical File

Common Settings (Mandatory)
Input Directory
BIDS Root Directory	/
ROIs Directory	/
T1 Anatomical Image Identifiers	Desc Space
Lesion Mask Identifiers	Suffix Space Label
Subject
Session
White Matter Segmentation Directory	/
Lesion Root Directory	/
Multiprocessing

Output Settings
Output Directory
Start Registration Space
Output Registration Space
Registration Transform
Reorient
Brain Registration
Lesion Corrected

Configuration for Brain Extraction
Mask
Fraction

Configuration for registration with FLIRT
Cost Function
Reference	/

Configuration for Lesion Correction
Image Norm Min
Image Norm Max
White Matter Spread

Configuration for Heatmap
Transparency
Reference	/