T1Prep 0.4.0

T1 PREProcessing Pipeline (aka PyCAT)

Note: This project is still in development and may contain bugs. Please report issues if you encounter problems.

T1Prep: T1 PREProcessing Pipeline (aka PyCAT)

T1Prep is a Python pipeline for preprocessing and segmenting T1-weighted MRI data. It supports:

• Bias-field correction and denoising
• Brain extraction (skull stripping)
• Tissue segmentation (GM, WM, CSF)
• Cortical surface reconstruction and thickness estimation
• Non-linear spatial registration to MNI152 space
• Atlas-based ROI extraction
• White matter hyperintensity (WMH/lesion) detection
• BIDS derivatives output naming

Cortical surface reconstruction uses the cat-surf Python package (pure Python bindings to the CAT-Surface C library — no compiled binaries required).

For full documentation, CLI usage, Docker instructions, and helper scripts see the GitHub repository.

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Installation

pip install T1Prep

Download model weights

Model weights are not bundled in the wheel (they are ~500 MB). Download them after installation:

t1prep-download-models

Models are stored alongside the deepmriprep package data and are downloaded automatically on first pipeline use if this step is skipped.

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Requirements

• Python 3.9–3.12
• ~2 GB disk space for model weights (downloaded separately, see above)
• For GPU acceleration: CUDA-capable GPU or Apple Silicon (MPS)

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Python API

from t1prep import run_t1prep

# Single file — results saved next to input
run_t1prep("/data/sub-01_T1w.nii.gz")

# Single file, BIDS-compatible output
run_t1prep("/data/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz", bids=True)

# Batch processing with options
run_t1prep(
    ["/data/T1/sub-01.nii.gz", "/data/T1/sub-02.nii.gz"],
    out_dir="/results",
    atlas=["neuromorphometrics", "suit"],
    multi=-1,          # auto-detect parallelism
    wp=True,           # save warped segmentations
    p=True,            # save native segmentations
    csf=True,          # save CSF segmentation
    lesions=True,      # save WMH lesion map
    gz=True,           # compress outputs (.nii.gz)
    stream_output=True,
    log_file="/results/T1Prep_run.log",
)

Key parameters

Parameter	Type	Description
files	str or list[str]	Input NIfTI file(s)
out_dir	str	Output directory (default: same as input)
atlas	list[str]	Atlas names for ROI extraction
surf	bool	Run cortical surface estimation (default: True)
multi	int	Parallel workers; -1 = auto (default: 1)
bids	bool	Use BIDS derivatives naming
gz	bool	Save compressed NIfTI (.nii.gz)
wp	bool	Save warped (MNI space) segmentations
p	bool	Save native space segmentations
csf	bool	Save CSF segmentation
lesions	bool	Save WMH/lesion map
amap	bool	Use AMAP segmentation (CAT12-style)
skullstrip_only	bool	Only run skull stripping then exit
skip_skullstrip	bool	Skip skull stripping (pre-stripped input)

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Output structure

Non-BIDS (default): subfolders mri/, surf/, report/, label/ in the output directory, with CAT12-compatible filenames (e.g., mwp1sub-01.nii, lh.thickness.sub-01).

BIDS (with bids=True): BIDS derivatives layout <out_dir>/derivatives/T1Prep-v<version>/sub-XX/ses-YY/anat/.

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License

Distributed under the Apache License 2.0.