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[ENH] Adds extraction of physio signals from DICOMs #446

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[ENH] Adds extraction of physio signals from DICOMs #446

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Commits on May 5, 2020

  1. [ENH] Adds extraction of physio signals from DICOMs 

    It uses [`bidsphysio`](https://github.com/cbinyu/bidsphysio) to extract physiological signals from CMRR EPI DICOMs.

It includes regression test
    @pvelasco
    pvelasco committed May 5, 2020
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  2. Adds heuristic for physio extraction.

    @pvelasco
    pvelasco committed May 5, 2020
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Commits on May 6, 2020

  1. Moves the installation of bidsphysio to info.py 

    ... from `Dockerfile`
    @pvelasco
    pvelasco committed May 6, 2020
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  2. Minor formating in heudiconv/convert.py 

    Co-authored-by: Mathias Goncalves <[email protected]>
    @pvelasco @mgxd
    pvelasco and mgxd authored May 6, 2020
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  3. Minor formating in heudiconv/convert.py 

    Co-authored-by: Mathias Goncalves <[email protected]>
    @pvelasco @mgxd
    pvelasco and mgxd authored May 6, 2020
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  4. Minor formating in heudiconv/dicoms.py 

    Co-authored-by: Mathias Goncalves <[email protected]>
    @pvelasco @mgxd
    pvelasco and mgxd authored May 6, 2020
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  5. Minor formatting updates

    @pvelasco
    pvelasco committed May 6, 2020
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  6. Minor formatting updates

    @pvelasco
    pvelasco committed May 6, 2020
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  7. Adds assert_cwd_unchanged to test_regression

    @pvelasco
    pvelasco committed May 6, 2020
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  8. RF: convert - convert_physio returns if bids_options is None 

    That reduces indentation in the function code.
    @pvelasco
    pvelasco committed May 6, 2020
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Commits on Jan 6, 2021

  1. ENH: Adds "AcquisitionTime" to the seqinfo

    @pvelasco
    pvelasco committed Jan 6, 2021
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Commits on Jan 7, 2021

  1. Switch back order of seqinfo_fields 

    To preserve backwards compatibility
    @pvelasco
    pvelasco committed Jan 7, 2021
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Commits on Jan 8, 2021

  1. Switch back order of SeqInfo arguments in dicom.py 

    To preserve backwards compatibility
    @pvelasco
    pvelasco committed Jan 8, 2021
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  2. Adds unittest to check "time" in the right position in dicominfo.tsv

    @pvelasco
    pvelasco committed Jan 8, 2021
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  3. ENH: Allows the user to save the Phoenix Report (Siemens) in the sour… 

    …cedata

This way the user can go back to the scanner and import the exact same protocol that was run for a given subject, improving reproducibility.
    @pvelasco
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  4. Changed calls to bidsphysio to conform with newest version 

    [`bidsphysio`](https://github.com/cbinyu/bidsphysio) has been refractored into subpackages so that now we only need to import `bidsphysio.dcm2bids`, which has fewer dependencies
    @pvelasco
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  5. Merge branch 'master' into dcm_physio

    @pvelasco
    pvelasco authored Jan 8, 2021
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Commits on Jan 12, 2021

  1. BF(py3.5): explicitly case path to str for open

    @yarikoptic
    yarikoptic authored Jan 12, 2021
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  2. ENH(minor): sort imports

    @yarikoptic
    yarikoptic committed Jan 12, 2021
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Commits on Jan 19, 2021

  1. Merge pull request #6 from cbinyu/adds_acq_time_to_seqinfo 

    Merges `adds_acq_time_to_seqinfo` into `dcm_physio` branch
    @pvelasco
    pvelasco authored Jan 19, 2021
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  2. Merge branch 'dcm_physio' into handles_phoenix_file

    @pvelasco
    pvelasco authored Jan 19, 2021
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  3. Merge pull request #7 from cbinyu/handles_phoenix_file 

    Merge `handles_phoenix_file` into `dcm_physio`
    @pvelasco
    pvelasco authored Jan 19, 2021
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Commits on Jan 21, 2021

  1. Add environment marker (Py>3.5) for dcm2bids requirement. 

    The dependencies for `bidsphysio.dcm2bids>=1.4.3` require Python 3.6 or higher, so don't try to install `bidsphysio.dcm2bids` unless `python_version > 3.5`.
    @pvelasco
    pvelasco committed Jan 21, 2021
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  2. Change name of extra_requires from dcm2bids to physio 

    Thanks to @tsalo for his suggestion
    @pvelasco
    pvelasco committed Jan 21, 2021
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Commits on Jan 22, 2021

  1. Delete some unneeded checks in the bids_physio heuristic.

    @pvelasco
    pvelasco committed Jan 22, 2021
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