Pipeline Outputs¶

This page describes the files produced by DCEPrep's preprocessing and analysis phases.

Directory Structure¶

Outputs are written to a derivatives/ folder alongside your rawdata/, following BIDS derivative conventions:

rawdata/
derivatives/
└── sub-01/
    └── ses-01/
        ├── anat/
        ├── dce/
        ├── case_report.html
        └── [comparison_name]/     ← if using -C flag
            ├── anat/
            └── dce/
population_report.html             ← at derivatives root

Preprocessing Outputs¶

Core outputs¶

File	Description
`dce/sub-##_ses-##_desc-bfcz_DCE.nii.gz`	Final preprocessed DCE: bias-corrected (`b`), z-normalized (`z`)
`anat/sub-##_ses-##_space-DCEref_T1map.nii`	Quantitative T1 map registered to DCE space
`anat/sub-##_ses-##_space-DCEref_VFA.nii.gz`	VFA image registered to DCE space
`dce/sub-##_ses-##_desc-AIF_T1map.nii.gz`	AIF mask in T1 map space
`anat/sub-##_ses-##_space-DCEref_desc-brain_mask.nii.gz`	Brain mask in DCE space

Intermediate files¶

File	Description
`dce/sub-##_ses-##_desc-hmc_DCE.nii`	Head-motion-corrected DCE (before bias/z-norm)
`anat/sub-##_ses-##_space-DCEref_T1w.nii.gz`	MPRAGE registered to DCE space
`anat/sub-##_ses-##_space-DCEref_T1w.mat`	MPRAGE → DCE affine transform
`anat/sub-##_ses-##_label-WM_mask.nii.gz`	White matter segmentation mask
`anat/sub-##_ses-##_space-DCEref_label-WM_mask.nii.gz`	WM mask in DCE space

Analysis Outputs¶

Quantitative maps¶

File	Description
`sub-##_ses-##_Ktrans.nii`	Volume transfer constant Ktrans (min⁻¹); primary BBB permeability measure
`sub-##_ses-##_vp.nii`	Plasma volume fraction vp (unitless)

Reports¶

File	Description
`case_report.html`	Per-case QC report (self-contained HTML with embedded images)
`population_report.html`	Population-level summary (outliers, group stats, spreadsheet export)

QC figures¶

File	Description
`*_ktrans_analysis.png`	Slice-by-slice Ktrans statistics plots
`*_ktrans_report.png`	Multi-panel Ktrans slice visualization
`*_motion.png`	Motion parameter plots (if `-m` was used)

Naming Conventions¶

DCEPrep follows BIDS-derivative naming conventions:

desc-bfcz — bias field corrected (bfc) + z-normalized (z)
desc-hmc — head motion corrected
space-DCEref — registered to the DCE reference volume
label-WM — white matter label/mask
desc-AIF — arterial input function mask

Comparison Mode Outputs¶

When using -C [name], all outputs are written into a named subdirectory:

derivatives/sub-01/ses-01/
├── noMC/               ← -C noMC
│   ├── anat/
│   └── dce/
└── fullPrep/           ← -C fullPrep
    ├── anat/
    └── dce/

This allows side-by-side comparison of runs with different preprocessing choices. See Comparison Mode.

Spreadsheet Export¶

The population report generates a .xlsx spreadsheet in the derivatives root containing per-subject summary statistics for all Ktrans and T1 metrics. This file is suitable for direct import into statistical analysis software.

File location¶

derivatives/spreadsheets/dataset_ktrans_YYYY-MM-DD.xlsx

Sheets¶

Sheet	Contents
Success	All cases that completed processing and passed automated QC
Pre-Exclude	Cases auto-flagged for excessive motion (> 3.8 mm displacement) or low AIFitness (< 59)
Fail	Cases that failed processing (missing files, wmparc errors, etc.)
Missing	Cases expected but not found in the derivatives

Each sheet is indexed by Subject_ID (format: sub-##_ses-##).

Columns (Success sheet)¶

The spreadsheet contains the following column groups:

Group	Columns
Demographics	Date, APOE, Sex, Age
Scanner	Machine, Institution, Coil
Acquisition	TR, Time_resolution, TE, Flip_angle, n_reps
QC	Approximate SNR, AIFitness, aif_fitted_r2, manual_aif_status, max_disp
T1	T1_blood, T1_wm_median, T1_gm_median
Ktrans	Ktrans_wm_median, Ktrans_gm_median, plus per-region medians (Hippo, PhG, Putamen, Pallidum, Thalamus, Caudate, Amygdala, Entorhinal cortex, Fusiform gyrus cortex/WM, Insula WM, Superior/Inferior temporal cortex, Posterior cingulate cortex, Medial temporal cortex)
Vp	Per-region Vp medians (same regions as Ktrans)
Volume	Per-region volumes in mm³ (same regions)
Cortical thickness	Per-region average and std thickness from FreeSurfer aparc (34 regions, bilateral average)

The Pre-Exclude and Fail sheets include an additional Reason column at the beginning.