docs/_check_preprocessing.qmd at main · HALFpipe/docs · GitHub

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1. In your working directory, copy and paste the whole block of code into your terminal session.

```bash
> incomplete-subject-list.txt
find "derivatives/halfpipe" -type d -path "*/func" | while read task_dir; do
 sub_id=$(echo "$task_dir" | grep -o "sub-[^/]*")
 file_count=$(find "$task_dir" -type f | wc -l)
 echo "$sub_id $file_count"
done | sort > count-files-subject-list.txt
echo "Done. See count-files-subject-list.txt for subject file counts."
```

2. There will be 2 generated files, an empty **incomplete-subject-list.txt** and a **count-files-subject-list.txt** file where Subject IDs and their output file counts are stored.
    a. Manually inspect **count-files-subject-list.txt** and the `derivatives/halfpipe` subjects folders to verify the list of subjects and their file counts.

    b. If any subjects have less than the expected amount of file (or differ from others) in **count-files-subject-list.txt** they will likely need to be re-run.

    c. We recommend checking out the `err.txt` file and inspect the error messages, if any.

3. Rerun HALFpipe
    a. Run HALFpipe again, but add the option --subject-list `<path/to/incomplete-subject-list.txt>` to the end of the command. Then select **Run without modification**.