README.md

• bidsNighres
  • Installation
    • Install Nighres
      • Set up java
      • Install java
  • Running the app

bidsNighres

BIDS app to help preprocessing high-res anatomical data using nighres.

Installation

Nighres is already part of this repo as a submodule added like this.

cd lib
git submodule add https://github.com/nighres/nighres.git

Install Nighres

See here.

Summary below!

Set up java

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 jcc

Install java

cd lib/nighres
./build.sh
python3 -m pip install .

Running the app

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