/docker-fix

Primary LanguageShell

docker-fix

  • A container for FSL-FIX

How to use this container

  • cd to the working directory in which you have fMRI and T1 data

  • Pull the image and mount working directory as /home/brain in the container

docker run -it --rm -v $PWD:/home/brain kytk/docker-fix:latest

  • Option 1: Run the "individual-fix_func_t1w.sh"

    • You specify functional and sturctural images individually.
cd # cd to /home/brain
cp /usr/local/bin/individual-fix_func_t1w.sh .
(edit the script)
./individual-fix_func_t1w.sh <func.nii.gz> <struct.nii.gz>

  • Option 2: Run the "individual-fix.sh" script

    • This script assumes that the filename of fMRI data starts with F_, and T1 data starts with V_ and shares the same ID. e.g. F_subj1.nii.gz and V_subj1.nii.gz
cd # cd to /home/brain
individual-fix.sh F_*.nii.gz
  • Then the script runs MELODIC for fMRI data and FIX after that with default parameter (Stardard.R 20 -m).
    • The result data would be "filtered_func_data_clean.nii.gz" under *.ica