Testing strategy

[tsalo]

I'm going to put together a couple of versions of raw + derivatives datasets for tests. Each limited to 100 volumes:

1. fMRIPrep derivatives with the required files in boldref space and MNI152NLin6Asym space. Plus confounds.
2. fMRIPrep derivatives with the required files in MNI152NLin6Asym space only, plus confounds.
3. Raw + fMRIPrep derivatives with the required files in boldref space only, plus confounds.
4. Raw + fMRIPrep derivatives with transforms to MNI152NLin6Asym and confounds.
   • This is distinct from #12 because minimal mode doesn't output confounds. I think this is more equivalent to either resampling mode (not 100% sure there are confounds with resampling mode) or running fMRIPrep without MNI152NLin6Asym as an output space.
   • resampling mode doesn't produce confounds.

[tsalo]

Here were the settings I used:

      --participant-label 01 \
      --level full \
      --output-spaces func MNI152NLin6Asym:res-2 \
      --output-layout bids \
      --fs-license-file /license.txt \
      --skip_bids_validation \
      --bids-filter-file ${CODE_DIR}/filter.json"

The filter just specified the session ID, since ds005115 has like 40 sessions.

Then I went through, removed sourcedata, and removed what that seemed appropriate for each test configuration. The one thing I'm not sure about is, does fMRIPrep output the boldref-space brain mask if you don't specify boldref-space outputs?

[tsalo]

Local testing:

• mni6 means there are fMRIPrep derivatives in MNI152NLin6Asym:res-2 space. nomni6 means there are no MNI152NLin6Asym-space derivatives, but I didn't remove the T1w-to-MNI152NLin6Asym transform since that should still be available.
• func means there are fMRIPrep derivatives in func:res-native space. nofunc means there's no boldref-space preprocessed BOLD file (I didn't remove the boldref-space brain mask).
• raw means I provided the raw BIDS datasets as the input dataset, and the fMRIPrep derivatives as a --derivatives dataset.

Results:

• [X] mni6-func-raw (had to fix a bug)
• [X] mni6-func-noraw
• [x] mni6-nofunc-raw
• [x] mni6-nofunc-noraw
• [ ] nomni6-func-raw
• [ ] nomni6-func-noraw
• [ ] nomni6-nofunc-raw
• [ ] nomni6-nofunc-noraw (don't expect to work)

[tsalo]

The resampling workflow isn't working, even for hardcoded transforms, so all of the nomni6 tests are failing. The hard part is the field map.

EDIT: I forgot to assign IntendedFor in the dataset before running fMRIPrep, so there wasn't any distortion correction anyway. I need to re-run fMRIPrep after fixing that 🤦