Output Directory Structure

Target Audience

Neuroimaging researchers interpreting pipeline outputs.

The pipeline creates a structured output hierarchy under <path>/<subject_id>/. This page describes the full directory layout and the key files produced at each location.

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Top-Level Layout

<path>/<subject_id>/
├── raw/
│   └── anatMRI/
│       ├── T1/
│       │   ├── T1_orig.nii.gz          # original input copy
│       │   └── T1_orig_defaced.nii.gz  # defaced original (if --nodefacing not set)
│       └── T2/
│           ├── T2_orig.nii.gz
│           └── T2_orig_defaced.nii.gz
├── analysis/
│   └── anatMRI/
│       ├── T1/
│       │   ├── preproc/
│       │   ├── processed/
│       │   ├── temp/                   # removed after pipeline completes
│       │   └── log/
│       └── T2/
│           ├── preproc/
│           ├── processed/
│           └── temp/
└── log/

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T1 Preprocessed Outputs (analysis/anatMRI/T1/preproc/)

Sub-folder	Key Files	Description
reg/	T1_2_std.mat	T1 → MNI linear affine matrix
reg/	std_2_T1.mat	MNI → T1 inverse affine
reg/	T1_2_std_warp_field.nii.gz	T1 → MNI non-linear warp (RegType 2/3)
reg/	T1_2_std_warp_coeff.nii.gz	FNIRT warp coefficients (RegType 2 only)
reg/	std_2_T1_warp_field.nii.gz	MNI → T1 inverse warp
bias/	T1_brain_bias.nii.gz	FAST-estimated bias field
SIENAX/	report.sienax	Brain volume report (mm³)
qc/	(optional)	Quality control outputs

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T1 Processed Outputs (analysis/anatMRI/T1/processed/)

Sub-folder	Key Files	Description
data/	T1.nii.gz	Cropped, reoriented T1 (not bias-corrected)
data/	T1_brain.nii.gz	Skull-stripped T1
data/	T1_brain_mask.nii.gz	Binary brain mask
data/	T1_unbiased.nii.gz	Bias-corrected whole-head T1
data/	T1_unbiased_brain.nii.gz	Bias-corrected skull-stripped T1
data2std/	T1_2_std.nii.gz	T1 in MNI152 space (linear)
data2std/	T1_2_std_brain_lin.nii.gz	Brain-only T1 in MNI (linear)
data2std/	T1_2_std_warped.nii.gz	T1 in MNI152 space (non-linear)
data2std/	T1_2_std_brain_warped.nii.gz	Brain-only T1 in MNI (non-linear)
seg/tissue/sing_chan/	T1_pve_CSF.nii.gz	CSF partial volume estimate
seg/tissue/sing_chan/	T1_pve_GM.nii.gz	Grey matter partial volume estimate
seg/tissue/sing_chan/	T1_pve_WM.nii.gz	White matter partial volume estimate
seg/tissue/sing_chan/	T1_{CSF,GM,WM}_mask.nii.gz	Thresholded binary tissue masks
seg/tissue/sing_chan/	T1_pveseg.nii.gz	FAST hard segmentation (integer labels)
seg/tissue/multi_chan/	T1_pve_{CSF,GM,WM}.nii.gz	Joint T1+T2 FAST segmentation (if T2 provided)
seg/sub/	T1_subcort_seg.nii.gz	FIRST subcortical segmentation (if --subseg)
FreeSurfer/	Full recon-all output	FreeSurfer subject directory (if --freesurfer)
FastSurfer/	Full FastSurfer output	FastSurfer subject directory (if --fastsurfer)

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T2 Outputs (analysis/anatMRI/T2/)

Path	Key Files	Description
processed/data/	T2.nii.gz	T2 aligned to T1 native space
processed/data/	T2_brain.nii.gz	Skull-stripped T2
processed/data/	T2_unbiased.nii.gz	Bias-corrected T2
processed/data2std/	T2_2_std.nii.gz	T2 in MNI space (linear)
processed/data2std/	T2_2_std_warped.nii.gz	T2 in MNI space (non-linear)
preproc/reg/	T2_2_std.mat	T2 → MNI affine
preproc/lesions/	final_mask.nii.gz	Binary WM lesion mask (BIANCA)
preproc/lesions/	volume.txt	Lesion volume in voxels

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Log Files

A log file is created at analysis/anatMRI/T1/log/log.txt and captures all processing steps, timestamps, software versions, and parameter values.