[ENH] adapt workflows to new bids-matlab

[Remi-Gau]

fixes #369

[codecov]

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❗ No coverage uploaded for pull request base (fmriprep_input@015bd1d). Click here to learn what that means.
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@@                Coverage Diff                @@
##             fmriprep_input     #368   +/-   ##
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  Coverage                  ?   58.28%           
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  Files                     ?      116           
  Lines                     ?     1889           
  Branches                  ?        0           
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  Hits                      ?     1101           
  Misses                    ?      788           
  Partials                  ?        0           

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