DCEMapper is an open-source desktop application built for researchers and clinicians working with Dynamic Contrast Enhancement (DCE) MRI data. It covers the full analysis pipeline — loading raw or BIDS-structured NIfTI files, applying preprocessing filters, drawing ROIs, and generating semi-quantitative parametric maps — all within a single PyQt6-based graphical interface.Documentation Index
Fetch the complete documentation index at: https://mintlify.com/Rubick65/dcemapper/llms.txt
Use this file to discover all available pages before exploring further.
Introduction
Learn what DCEMapper is, who it’s for, and how it fits into a DCE-MRI workflow.
Installation
Install DCEMapper on Windows via the pre-built executable or set up from source with Conda.
Quickstart
Open your first NIfTI file, explore slices, and generate your first parametric map in minutes.
User Guide
Step-by-step walkthroughs for every feature: data loading, preprocessing, ROI tools, and more.
What DCEMapper Does
DCEMapper provides an end-to-end workflow for DCE-MRI analysis:Load your data
Open NIfTI files directly, load a full BIDS dataset, convert raw Bruker data, or reload previously processed outputs.
Preprocess
Apply denoising filters (ASCM, Non-Local Means, MP-PCA, Local PCA) and Gibbs artifact suppression to clean your images before analysis.
Define your ROI
Draw rectangular, elliptical, or polygonal regions of interest on individual slices. Save and reload masks for reproducible analysis sessions.
Key Features
Multi-format Data Loading
BIDS datasets, single NIfTI files, processed outputs, and Bruker raw data conversion — all from the File menu.
Denoising & Artifact Removal
Five denoising algorithms plus Gibbs suppression, each with configurable parameters and interactive before/after preview.
Interactive ROI Tools
Rectangle, ellipse, and polygon selectors with smooth Gaussian edges. Save masks as NIfTI files and reload them later.
Semi-Quantitative Mapping
Compute RCE, RCEmax, and Time-to-Peak maps and export them as standard NIfTI files ready for downstream analysis.
Voxel Intensity Curves
Click any voxel in the main canvas to plot its signal intensity time-series and log coordinates with intensity increase.
Keyboard Shortcuts
Full shortcut coverage for navigation, ROI tools, zoom, pan, playback, and fullscreen.
Explore the Reference
I/O API
Functions for loading NIfTI files and extracting slice arrays.
Preprocessing API
Denoising and Gibbs removal function signatures and parameters.
Processing API
Semi-quantitative mapping functions: RCE, RCEmax, TTP calculations.
ROI API
Mask update functions for rectangular, elliptical, and polygonal ROIs.