diff --git a/README.md b/README.md index 72b3bac..c15f5c7 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,16 @@ This pipeline is an open-source pipeline for MRI image segmentation, registratio The current code uses the [command line interface](https://www.computerhope.com/jargon/c/commandi.htm) for use. Pull requests for a GUI to command-line translation are welcome. +## Overview +This repo is to serve as an open-source location for developers to add MRI processing techniques. This includes, but is not limited to: +- image processing tasks (denoising, super-resolution, segmentation, etc) +- relaxation parameter analysis (T1, T1-rho, T2, T2*, etc) +- anatomical features (patellar tilt, femoral cartilage thickness, etc) + +We hope that this open-source pipeline will be useful for quick anatomy/pathology analysis from MRI and will serve as a hub for adding support for analyzing different anatomies and scan sequences. + ## Supported Features +Currently, this pipeline supports analysis of the femoral cartilage in the knee using cubequant, cones, and [DESS](https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.26577) scanning protocols. Details are provided below. ### Scans The following scan sequences are supported. All sequences with multiple echos, spin_lock_times, etc. should have metadata in the dicom header specifying this information. @@ -104,6 +113,11 @@ optional arguments: -t2_star quantify t2_star ``` +## Machine Learning Disclaimer +All weights/parameters trained for any task are likely to be most closely correlated to data used for training. If scans from a particular sequence were used for training, the performance of those weights are likely optimized for that specific scan type. As a result, they may not perform as well on segmenting images acquired using different scan types. + +If you do train weights for any deep learning task that you would want to include as part of this repo, please provide a link to those weights and detail the scanning parameters/sequence used to acquire those images. All data contributed to this pipeline should be made freely available to all users. + ## Use cases We detail use cases that could be useful for analyzing data. We assume that all scans are stored per patient, meaning that the folder structure looks like below: @@ -131,7 +145,7 @@ All use cases assume that the [current working directory](https://www.computerho #### Case 1 *Analyze patient01 knee T2 properties using DESS sequence* -1. Calculate 3D t2 map +1. Calculate 3D T2 map ``` python -m pipeline -d research_data/patient01/dess -s research_data/patient01/data dess -t2 ``` @@ -141,7 +155,7 @@ python -m pipeline -d research_data/patient01/dess -s research_data/patient01/da python -m pipeline -d research_data/patient01/dess -s research_data/patient01/data dess -rms segment --weights_dir unet_weights ``` -3. Calculate T_2 time for femoral cartilage +3. Calculate T2 time for femoral cartilage ``` python -m pipeline -l research_data/patient01/data -s research_data/patient01/data knee -fc -t2 ```