Giovanna Nordio - August 2023 Rubaida Easmin - September 2023
Scripts go in the scripts directory.
Library code (Python modules) goes in the findoutlie directory.
You should put the code in this findoutlie directory on your Python PATH.
This README file has instructions on how to get, validate and process the data.
cd data
curl -L https://figshare.com/ndownloader/files/34951602 -o group_data.tar
tar xvf group_data.tar
Add the hash_list file to Git:
git add data/group-*/hash_list.txt
git commit -m "Add hash list file"
Change directory back to root of repository
cd ..
Add the hash_list file to Git:
git add group-*/hash_list.txt
git commit -m "Add hash list file"
Change directory back to root of repository
cd ..
python3 scripts/validate_data.py data
python3 scripts/find_outliers.py data
This should print output to the terminal of form:
<filename>, <outlier_index>, <outlier_index>, ...
<filename>, <outlier_index>, <outlier_index>, ...
Where <filename> is the name of the image that has outlier scans, and
<outlier_index> is an index to the volume in the 4D image that you have
identified as an outlier. 0 refers to the first volume. For example (these
outlier IDs are completely random, for illustration):
data/sub-01/func/sub-01_task-taskzero_run-01_bold.nii.gz, 3, 21, 22, 104
data/sub-01/func/sub-01_task-taskzero_run-02_bold.nii.gz, 11, 33, 91
data/sub-03/func/sub-03_task-taskzero_run-02_bold.nii.gz, 101, 102, 132
data/sub-08/func/sub-08_task-taskzero_run-01_bold.nii.gz, 0, 1, 2, 166, 167
data/sub-09/func/sub-08_task-taskzero_run-01_bold.nii.gz, 3