dti-alps 0.1.0

Automatic DTI-ALPS ROI detection and analysis

autoDTI-ALPS

Automated DTI-ALPS (Diffusion Tensor Imaging Along the Perivascular Space) analysis tool. Uses template-based registration to place ROIs in projection and association fiber regions, then calculates the DTI-ALPS index from diffusion tensor imaging data.

Dependencies

Python

Requires Python 3.10+.

Core dependencies (installed automatically):

• NumPy
• NiBabel
• SciPy

Optional GUI dependencies (pip install -e ".[gui]"):

• Matplotlib
• Pillow

External Neuroimaging Software

The following third-party programs must be installed and available on your system PATH.

MRtrix3 (required)

MRtrix3 provides tools for diffusion MRI preprocessing and tensor fitting.

Command	Pipeline Stage	Purpose
dwidenoise	Denoising	Marchenko-Pastur PCA thermal noise removal
mrdegibbs	Gibbs Removal	Gibbs ringing artifact correction
dwifslpreproc	Preprocessing	Eddy current, motion, and distortion correction
dwi2tensor	Tensor Fitting	Fit diffusion tensor model to DWI data
tensor2metric	Metric Extraction	Extract FA, eigenvectors (V1-V3), and eigenvalues (L1-L3)
dwi2mask	Preprocessing	Brain mask generation from DWI
dwiextract	B0 Extraction	Extract b=0 volumes from DWI
mrmath	B0 Extraction	Average multiple b=0 volumes
mrconvert	Format Conversion	Image format conversion and header manipulation

Installation: https://www.mrtrix.org/download/

FSL (required)

FSL provides tools for brain extraction, registration, and image manipulation.

Command	Pipeline Stage	Purpose
flirt	Registration	Linear (affine) FA-to-template registration
fnirt	Registration	Non-linear FA-to-template registration
invwarp	Registration	Generate inverse warp field for ROI transformation
applywarp	ROI Placement	Transform ROI templates from standard to native space
fslmaths	Masking	Apply brain mask to FA image
eddy	Preprocessing	Eddy current and motion correction
topup	Preprocessing	Susceptibility-induced distortion field estimation
applytopup	Preprocessing	Apply topup distortion correction

Installation: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation

Installation

Whichever route you choose, MRtrix3 and FSL are not bundled and must be installed separately and on your PATH (see External Neuroimaging Software).

Install with pipx (recommended)

If you have Python 3.10+, pipx installs the app into an isolated environment and puts the dti-alps command on your PATH:

pipx install dti-alps
dti-alps            # launch the GUI

Update with pipx upgrade dti-alps. (Plain pip install dti-alps also works, ideally inside a virtualenv, and provides the same dti-alps command.)

Download the AppImage (no Python needed)

For double-click file with no Python setup, grab the latest Linux AppImage from the Releases page:

chmod +x dti-alps-*-x86_64.AppImage
./dti-alps-0.1.0-x86_64.AppImage

The AppImage bundles the app and its Python dependencies. To update, download the newer AppImage and replace the old file.

Qt runtime note: the GUI uses Qt 6, which needs libxcb-cursor0 on the host. If the app fails to start with an xcb platform-plugin error, install it: sudo apt install libxcb-cursor0 (Debian/Ubuntu).

From source (development)

pip install -e ".[gui]"

Usage

dti-alps                    # Launch GUI (default)
dti-alps --viewer           # Launch Results Viewer
dti-alps --viewer /path     # Launch viewer with specific output folder
dti-alps --report /path     # Generate quality reports
dti-alps --reanalyze /path --sphere 3  # Reanalyze with different ROI shapes

When running the AppImage, substitute ./dti-alps-*.AppImage for dti-alps; all CLI flags are forwarded (e.g. ./dti-alps-*.AppImage --viewer /path).