Pipeline Steps Reference¶

Quick-reference summary of all steps in both pipeline phases.

Preprocessing (`preprocess_all.sh`)¶

Step	Name	Tool	Flag Required
1	Brain extraction	HD-BET	— (always runs)
2	DCE head motion correction	FSL `mcflirt`	`-m`
3	MPRAGE → DCE registration	ANTs `antsRegistration`	— (always runs)
4	VFA → DCE registration	ANTs `antsRegistration`	— (always runs)
5	MPRAGE white matter segmentation	FSL `fast`	— (always runs)
6	Apply MPRAGE → DCE transform to WM mask	ANTs `antsApplyTransforms`	— (always runs)
7	VFA bias field correction (1st round)	FSL `fast`	`-b`
8	VFA z-axis normalization	`VFA_norm.py`	`-Z`
9	VFA bias field correction (2nd round)	FSL `fast`	`-B`
10	T1 map generation	ROCKETSHIP / MATLAB	— (always runs)
11	Apply MPRAGE → DCE transform to brain mask	ANTs `antsApplyTransforms`	— (always runs)
12	AIF selection	`AutoAIF` neural network	`-A`
13	DCE bias field correction	FSL `fast`	`-b`
14	DCE z-axis normalization	`DCE_norm.py`	`-Z`

Step	Name	Tool	Flag Required
0	DCE smoothing	`iNESMA_GPU.py` (CUDA)	`-S`
1	Ktrans mapping	ROCKETSHIP / MATLAB	— (always runs)
2	GM & CSF masking	ANTs + FSL `fslmaths`	— (always runs)
2a	FreeSurfer WM parcellation	FreeSurfer	`-f`
3	QC analysis	`ktrans_analysis.py`, `ktrans_report.py`	— (always runs)
4	Case report generation	`case_report.py`	— (always runs)
5	Population report generation	`population_report.py`	— (always runs, after all cases)