The processed T1 maps have been uploaded in the RRSG/qMRSG 2020 ISMRM Challenge OSF.io repository, under the folder challenge_t1_maps. The folders are organised in the same structure as the challenge_submissions folder, which contain the raw data. Each T1 map zip file contains 1) T1 maps, 2) YAML/JSON configuration files that contain the challenge submissions details, 3) T1 maps saved as PNG images for quality assurance purposes, and 4) a text file with the link to the raw data used to fit the accompanying T1 map.
Coming soon.
These instructions were tested on a Macbook, and will likely be identical for Linux. The syntax for Windows might be different, depending on the shell you're using to install the Python packages. The shell that comes with Anaconda would likely work well.
- Clone or download this GitHub repository
(Recommended) Create a conda virtual environment.
conda create -n sos_matlab python=3.6conda activate sos_matlabconda install ipython=7.2.0
Setup the MATLAB Engine API for Python
cd /Applications/MATLAB_R2018b.app/extern/engines/python/- Replace
MATLAB_R2018b.appwith whatever version of MATLAB you have.
- Replace
python setup.py install
Install neessary Python packages
pip install sos==0.21.6 sos-bash==0.12.3 sos-javascript==0.9.12.2 sos-julia==0.9.12.1 sos-matlab==0.18.4 sos-notebook==0.21.9 sos-python==0.9.12.1 sos-r==0.9.12.2 sos-ruby==0.9.15.0 sos-sas==0.9.12.3 scipy numpy imatlab;
Install the MATLAB and SOS Jupyter kernels
python -mimatlab installpython -m sos_notebook.install
Start a Jupyter session
jupyter notebook RRSG_T1_fitting.ipynb- Choose the configuration file you want to use in the first cell
- Run all cells
