BIDS app to help preprocessing high-res anatomical data using nighres.
Nighres is already part of this repo as a submodule added like this.
cd lib
git submodule add https://github.com/nighres/nighres.git
See here.
Summary below!
sudo apt-get install openjdk-8-jdk
export JCC_JDK=/usr/lib/jvm/java-8-openjdk-amd64
# this may fail when in a virtual environment
python3 -m pip install jcccd lib/nighres
./build.sh
python3 -m pip install .root_dataset=${PWD}/../../..
input_dataset=${root_dataset}/inputs/raw/
output_location=${root_dataset}/derivatives/bidsNighres/
filter_file=${root_dataset}/code/filter_file.json
echo ${input_dataset}
python run.py --input-datasets ${input_dataset} \
--output-location ${output_location} \
--analysis-level participant \
--participant-label pilot001 \
--action segment \
--bids-filter-file ${filter_file} \
--dry-run False