Qsiprep

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* Adds a flag for a BIDS filter file 256
* Fixes a bug where --dwi-only is selected along with --intramodal-template

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Many bugfixes

* Fix bug that produced flipped scalar images (251)
* Added a default working directory to prevent uninterpretable error message (250)
* Fix a bug in the `dipy_3dshore` reconstruction workflow (249)
* Remove hardlinking from DSI Studio interfaces (214)
* Add an option to use a BIDS database directory (247)
* Fix bug in interactive reports for HCP-style acquisitions (238)
* Update defaults for `Patch2Self` (230, 239)
* Remove cmake installer from docker image after compiling ANTS (229)

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This version introduces major changes to the TOPUP/eddy workflow. Feedback would be greatly
appreciated!

* Added new algorithm for selecting b=0 images for distortion corretion (202)
* Added the Patch2Self denoising method (203, credit to ShreyasFadnavis)
* Documentation has been expanded significantly (212)
* Boilerplate for DWI preprocessing is greatly expanded (200)

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Adds options for processing infant dMRI data. Also enables running without a T1w
image.

* Adds ``--dwi-only`` and ``--infant`` options to QSIPrep. (177)

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NEW: Workflow defaults have changed. T1w-based spatial normalization is done by
default (disabled by ``--skip-t1-based-spatial-normalization``) and dwi scans
are merged before motion correction by default (disabled by ``--separate-all-dwis``).

* Deprecate some commandline arguments, change defaults (168)
* Fix typo in workflow names (162)
* Fix bug from 0.10.0 where ODFs were not appearing in plots (160)

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* Adds support for oblique acquisitions (156)