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Remove sdcflows and model ASLPrep on fMRIPrep/next #338

Merged
merged 380 commits into from
Dec 6, 2023
Merged

Remove sdcflows and model ASLPrep on fMRIPrep/next #338

merged 380 commits into from
Dec 6, 2023
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Commits on Nov 15, 2023

  1. Try this.

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  2. keep working.

    @tsalo
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  3. Update plotting.py

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  4. Update base.py

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  5. Update base.py

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  6. Update.

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  7. Update plotting.py

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  8. Update plotting.py

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  9. fix.

    @tsalo
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  10. Update plotting.py

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  11. Update plotting.py

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Commits on Nov 16, 2023

  1. Update plotting.py

    @tsalo
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  2. Update.

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  3. Update cbf.py

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  4. Update cbf.py

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  5. Update cbf.py

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  6. Update cbf.py

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  7. Set Infs to 0. 

    The Philips M0 scan has values of zero for some in-mask voxels, which, when used to calculate CBF, results in Infs.
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  8. Try just using standard ASL preproc pipeline.

    @tsalo
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  9. Try that.

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  10. Update tests.py

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  11. Update outputs.py

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  12. Update base.py

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  13. Update base.py

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Commits on Nov 17, 2023

  1. More work.

    @tsalo
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  2. More work.

    @tsalo
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  3. More work.

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  4. Update utility.py

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  5. More work.

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Commits on Nov 20, 2023

  1. Run black and isort.

    @tsalo
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  2. Update.

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  3. Update.

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  4. More work.

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  5. Update.

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  6. Fix.

    @tsalo
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  7. Update gecbf.py

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  8. Update.

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  9. Update misc.py

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  10. Update fit.py

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  11. Update.

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  12. Update.

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  13. Fix?

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  14. Update fit.py

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  15. Update fit.py

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  16. Update fit.py

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  17. Update reference.py

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  18. Update reference.py

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  19. Update fit.py

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  20. Update fit.py

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  21. Whoops!

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  22. Update fit.py

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  23. Update fit.py

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  24. Update fit.py

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  25. Update fit.py

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  26. Update fit.py

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  27. Lots of changes.

    @tsalo
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  28. Update config.py

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  29. Update base.py

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  30. Update base.py

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  31. Update base.py

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  32. Update base.py

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  33. Update.

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  34. Update base.py

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  35. Update.

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  36. Update.

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  37. Update base.py

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  38. Update confounds.py

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  39. Update.

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  40. Update base.py

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  41. Update.

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  42. Update confounds.py

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  43. Update.

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  44. Update.

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  45. Update.

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  46. Update workflows.rst

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Commits on Nov 21, 2023

  1. Update fit.py

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  2. Use new fMRIPrep!

    @tsalo
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  3. Update.

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  4. Update.

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  5. update.

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  6. Update reference.py

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  7. Update.

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  8. Fix some things.

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  9. Fix many things.

    @tsalo
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  10. Try 3.10.

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  11. Update.

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  12. Bump build Docker image version.

    @tsalo
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Commits on Nov 22, 2023

  1. Update.

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  2. Update lint.yml

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  3. Update.

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  4. Update run.py

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  5. Update test_cli.py

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  6. Update test_cli.py

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  7. Update parser.py

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Commits on Nov 24, 2023

  1. Update parser.py

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  2. Update parser.py

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  3. Update parser.py

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  4. Update.

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  5. Update base.py

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  6. Update base.py

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  7. Update fit.py

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  8. Update fit.py

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  9. Update base.py

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  10. Update qc.py

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  11. Update apply.py

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  12. Update base.py

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  13. Update reference.py

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  14. Update base.py

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Commits on Nov 25, 2023

  1. Update base.py

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  2. Fix connections.

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Commits on Nov 26, 2023

  1. Make ApplyTransforms calls verbose.

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Commits on Nov 27, 2023

  1. Fix ApplyTransforms calls.

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  2. Try that.

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  3. Update.

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  4. Try fixing m0scan_native.

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  5. Try that then.

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  6. Try that then.

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  7. Update cbf.py

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  8. Update test_cli.py

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  9. Update aslprep_bids_config.json

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  10. Update test_cli.py

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  11. Write out native-space derivatives.

    @tsalo
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  12. Update outputs.py

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  13. Update expected outputs.

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  14. Update base.py

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Commits on Nov 28, 2023

  1. Update expected outputs.

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  2. Update.

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  3. Parcellate data no matter what.

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  4. More cleanup.

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  5. Try adding numpy to build requirements.

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  6. Run isort.

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  7. Update __init__.py

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  8. Deal with style issues.

    @tsalo
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  9. Add precomputed (will be empty).

    @tsalo
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  10. Ignore unused parameter.

    @tsalo
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  11. Try fixing install.

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  12. precomputed is a dictionary.

    @tsalo
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  13. Outsource more workflows to fmriprep.

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  14. Try to implement functional cache.

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  15. Update BASIL output names.

    @tsalo
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  16. Update base.py

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  17. Update hmc.py

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  18. Update bids.py

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  19. Remove GE workflows.

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  20. Try to fix GE HMC.

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  21. Whoops!

    @tsalo
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  22. Run isort.

    @tsalo
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  23. Update hmc.py

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  24. Update hmc.py

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  25. Update expected outputs.

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Commits on Nov 29, 2023

  1. Write out QC file.

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  2. Update utility.py

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  3. Add outputnode back in.

    @tsalo
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  4. Try to debug motion params more.

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  5. Support single-volume motion parameters.

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  6. Add source to docstring.

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  7. Keep cleaning up GE processing.

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  8. Set confounds min volumes to 2.

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  9. Update confounds.py

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  10. Make QC calculations flexible.

    @tsalo
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  11. Remove unused import.

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  12. Remove unused data files.

    @tsalo
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  13. Write out QC file correctly.

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  14. Rename QC json filename.

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  15. Add confounds to GE outputs.

    @tsalo
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  16. Drop unused functions and classes.

    @tsalo
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  17. Try fixing tests.

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  18. Use GenericLabel instead of MultiLabel.

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  19. Use fMRIPrep's resampling interfaces.

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  20. Remove unnecessary comment.

    @tsalo
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  21. Outsource more workflows to fMRIPrep.

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  22. Update expected_outputs_test_002.txt

    @tsalo
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  23. Update expected outputs.

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  24. Update expected_outputs_test_001.txt

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  25. Don't use FixHeadersApplyTransforms.

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Commits on Nov 30, 2023

  1. Fix some connections in fit.

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    tsalo committed Nov 30, 2023
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  2. Add checks.

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    tsalo committed Nov 30, 2023
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  3. Fix logger name.

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    tsalo committed Nov 30, 2023
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  4. Retain niftis for now.

    @tsalo
    tsalo committed Nov 30, 2023
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  5. Override DDS for some workflow calls.

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  6. Disable aslref-space outputs unless requested 

    Copies nipreps/fmriprep#3159.
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  7. Pass FLAIR images to anatomical workflow builder 

    Copied from nipreps/fmriprep#3146.
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  8. Tag memory estimates in resamplers 

    Copied from nipreps/fmriprep#3150.
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  9. Use M0 scan for reference for GE data.

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    tsalo committed Nov 30, 2023
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  10. Try to fix transform name.

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  11. Add reference image smoothing step.

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  12. Give smoothing output a BIDS-ish name.

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  13. Update fit.py

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  14. Remove unused modules.

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  15. Pin sMRIPrep version.

    @tsalo
    tsalo committed Nov 30, 2023
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  16. Reduce mask.

    @tsalo
    tsalo committed Nov 30, 2023
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  17. Squeeze masks before merging.

    @tsalo
    tsalo committed Nov 30, 2023
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  18. Fix module name.

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Commits on Dec 1, 2023

  1. Drop niftis from test outputs.

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  2. Update workflows.rst

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  3. Merge remote-tracking branch 'upstream/main' into remove-sdcflows-2

    @tsalo
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  4. Improve documentation.

    @tsalo
    tsalo committed Dec 1, 2023
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  5. Update api.rst

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  6. Update workflows.rst

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  7. Update citations.

    @tsalo
    tsalo committed Dec 1, 2023
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  8. More documentation improvements.

    @tsalo
    tsalo committed Dec 1, 2023
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  9. Remove dropped coverage files from expected outputs.

    @tsalo
    tsalo committed Dec 1, 2023
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  10. Update license and output docs.

    @tsalo
    tsalo committed Dec 1, 2023
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  11. Fix issues with CIFTI connections.

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    tsalo committed Dec 1, 2023
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Commits on Dec 2, 2023

  1. Update base Docker image. 

    The new version has MSM.
    @tsalo
    tsalo committed Dec 2, 2023
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  2. Add level testing jobs.

    @tsalo
    tsalo committed Dec 2, 2023
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  3. Update expected outputs.

    @tsalo
    tsalo committed Dec 2, 2023
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Commits on Dec 3, 2023

  1. Try fixing more issues.

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  2. Draft workflow to produce CIFTI CBF maps.

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    tsalo committed Dec 3, 2023
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  3. Keep working on CIFTI CBF workflow.

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Commits on Dec 4, 2023

  1. Keep working on CIFTI CBF workflow.

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  2. Add reference images.

    @tsalo
    tsalo committed Dec 4, 2023
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  3. Update outputs.py

    @tsalo
    tsalo committed Dec 4, 2023
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  4. Address multiple bugs with GIFTI outputs.

    @tsalo
    tsalo committed Dec 4, 2023
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  5. Try outputting fsaverage.

    @tsalo
    tsalo committed Dec 4, 2023
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  6. Add docstrings.

    @tsalo
    tsalo committed Dec 4, 2023
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  7. Ignore unused argument.

    @tsalo
    tsalo committed Dec 4, 2023
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  8. Update tests.

    @tsalo
    tsalo committed Dec 4, 2023
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  9. Fix!

    @tsalo
    tsalo committed Dec 4, 2023
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  10. Update test_002 cache (it was already v3).

    @tsalo
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  11. Update.

    @tsalo
    tsalo committed Dec 4, 2023
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  12. Update test_cli.py

    @tsalo
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  13. Update config.yml

    @tsalo
    tsalo committed Dec 4, 2023
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  14. Update config.yml

    @tsalo
    tsalo committed Dec 4, 2023
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  15. Fix things.

    @tsalo
    tsalo committed Dec 4, 2023
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  16. Update test_cli.py

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    tsalo committed Dec 4, 2023
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Commits on Dec 5, 2023

  1. Update config.yml

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  2. Combine QC and confounds modules.

    @tsalo
    tsalo committed Dec 5, 2023
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  3. Remove unused functions/interfaces.

    @tsalo
    tsalo committed Dec 5, 2023
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  4. Remove another unused function.

    @tsalo
    tsalo committed Dec 5, 2023
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  5. Remove unused interface function.

    @tsalo
    tsalo committed Dec 5, 2023
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  6. Bump anatomical test data version.

    @tsalo
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  7. Fix import.

    @tsalo
    tsalo committed Dec 5, 2023
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  8. Update expected outputs.

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  9. Create expected_outputs_qtab.txt

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  10. Grab MNI152NLin2009cAsym xfm for resampling.

    @tsalo
    tsalo committed Dec 5, 2023
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  11. Update expected outputs.

    @tsalo
    tsalo committed Dec 5, 2023
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  12. Add topup to boilerplate BibTeX file.

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  13. Revert some changes.

    @tsalo
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Commits on Dec 6, 2023

  1. Update expected outputs.

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  2. Move asl_anat_wf from resampling to full.

    @tsalo
    tsalo committed Dec 6, 2023
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  3. Try outputting CIFTI for one test.

    @tsalo
    tsalo committed Dec 6, 2023
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  4. Add updated fsLR workflow from fMRIPrep.

    @tsalo
    tsalo committed Dec 6, 2023
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  5. Update resampling.py

    @tsalo
    tsalo committed Dec 6, 2023
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  6. Speed up test_003.

    @tsalo
    tsalo committed Dec 6, 2023
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  7. Use internal version of init_bold_surf_wf.

    @tsalo
    tsalo committed Dec 6, 2023
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  8. Fix style issues.

    @tsalo
    tsalo committed Dec 6, 2023
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  9. Remove unused script.

    @tsalo
    tsalo committed Dec 6, 2023
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  10. Fix typos.

    @tsalo
    tsalo committed Dec 6, 2023
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  11. Drop CIFTI test and sort expected outputs.

    @tsalo
    tsalo committed Dec 6, 2023
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