White Matter Hypointensities lesions for T1-weighted MRI images.
It relies on a Convolutional Neural Network pre-trained on FLAIR segmentations using the large JPSC-AD cohort.
For background and technical details about its creation, refers to this corresponding Human Brain Mapping manuscript: http://doi.org/10.1002/hbm.25899
This program requires Python 3, with the PyTorch library, version > 1.4.0., although >=1.7 is highly recommended for improved memory usage
No GPU is required
Just clone or download this repository.
In addition to PyTorch, the code requires scipy and nibabel.
If not pre-installed, a simple way to install python3 from scratch may be to use a Anaconda (anaconda.com) environment then
- install scipy (
conda install scipyorpip install scipy) and nibabel (pip install nibabel) - get pytorch for Python/CPU from
https://pytorch.org/get-started/locally/. CUDA is not necessary.
To use the program, simply call:
./deepwmh.sh t1_image.nii.gz
(or it can be added to your PATH)
To process multiple subjects, pass them as multiple arguments.
deepwmh.sh subject_*.nii.gz.
The resulting WMH segmentation mask will be named t1_image_mask_wmh.nii.gz, and t1_image_mask_ROIs.nii.gz for the region labels (periventricular, deep-white, infracortical). The lesion total and regional volumes statistics are available in t1_image_wmh_in_lrois.csv.
If multiple input images were specified, a summary table is generated as all_subjects_wmh_report.csv
Optionally, adding "-v" (verbose) in the command line will output more images, including the non-thresholded (probabilistic, 0-255) WMH-lesion segmentation output, named t1_image_prob_wmh.nii.gz .
If the following message appears:
wgrid = self.grid @ self.tA
^
SyntaxError: invalid syntax
It probably means that the system python was found. Make sure python 3 is in your path or edit deepwmh.sh with a suitable path.