khanlab/LOBE_analysis

Snakemake workflow for LOBE study

lobe_analysis

before using, ensure you have pipx and poetry:

install pipx

python3 -m pip install --user pipx
python3 -m pipx ensurepath

install poetry

pipx install poetry

1. Clone repository

2. If using poetry/pipx:

poetry install
poetry shell

3. otherwise:

python3.11 -m venv venv
source venv/bin/activate
pip install .

To QC fmriprep data from zip files:

Use the -l (list) and pipe to less to find the filepaths you want to unzip, e.g.:

unzip -l  /home/ROBARTS/alik/graham/projects/ctb-akhanf-ab/cfmm-bids/Khan/LOBE/derivatives/snakebatch_LOBE_2024_03_19.zip  | less

Then, on /localscratch run:

unzip   /home/ROBARTS/alik/graham/projects/ctb-akhanf-ab/cfmm-bids/Khan/LOBE/derivatives/snakebatch_LOBE_2024_03_19.zip  "LOBE/derivatives/fmriprep_23.1.0/sub-*.html" "LOBE/derivatives/fmriprep_23.1.0/sub-*/figures/*"