run_order_fix.py is hard-coded to ses-baselineYear1Arm1

[ericearl]

What happened?

It looks like maybe ALL the data that isn't ses-baselineYear1Arm1 could be incorrectly ordered fMRI runs due to the hard-coded ses-baselineYear1Arm1 and the reliance on run_order_fix.py in unpack_and_setup.sh:

• https://github.com/DCAN-Labs/abcd-dicom2bids/blob/main/src/run_order_fix.py#L163-L164
• https://github.com/DCAN-Labs/abcd-dicom2bids/blob/main/src/unpack_and_setup.sh#L132-L145

What command did you use?

python run_order_fix.py --get-bids-errors --generate-map outputs/round_13/sub-NDARANONYMIZED outputs/round_13_sub-NDARANONYMIZED_error.json outputs/round_13_sub-NDARANONYMIZED_file_map.json --subject sub-NDARANONYMIZED

What version of abcd-dicom2bids are you using?

Our barely altered fork at https://github.com/nih-fmrif/abcd-dicom2bids.

Directory Structure

outputs/round_13/sub-NDARANONYMIZED
├── ses-2YearFollowUpYArm1
│   ├── anat
│   ├── dwi
│   ├── fmap
│   └── func
├── ses-4YearFollowUpYArm1
│   ├── anat
│   ├── dwi
│   ├── fmap
│   └── func
└── ses-baselineYear1Arm1
    ├── anat
    ├── dwi
    ├── fmap
    └── func

Relevant log output

> python run_order_fix.py --get-bids-errors --generate-map outputs/round_13/sub-NDARANONYMIZED outputs/round_13_sub-NDARANONYMIZED_error.json outputs/round_13_sub-NDARANONYMIZED_file_map.json --subject sub-NDARANONYMIZED
sub-NDARANONYMIZED
sub-NDARANONYMIZED
sub-NDARANONYMIZED
sub-NDARANONYMIZED
> head outputs/round_13_sub-NDARANONYMIZED_*.json
==> outputs/round_13_sub-NDARANONYMIZED_error.json <==
{"sub-NDARANONYMIZED": {"rest": {"current_order": [1, 2, 3, 4], "actual_order": [1, 4, 2, 3]}}}
==> outputs/round_13_sub-NDARANONYMIZED_file_map.json <==
{}

Add any additional information or context about the problem here.

I think run_order_fix.py is supposed to only print the BIDS participant ID once when it runs successfully. I am still trying to debug why it might be printing 4 times in my testing...