diagnostics-bold_but_better's Introduction

Diagnostics project

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.

It belongs to the Bold But Better group.

Get 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 ..

Check the data

python3 scripts/validate_data.py data

Find outliers

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

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