Mriqc

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* [FIX, CRITICAL] Do not chmod in Docker internal scripts
* FIX: Error creating derivatives folder
* ENH: Moved MNI spatial normalization to NIworkflows, and made robust.
* ENH: De-coupled participant and group (reports) levels
* ENH: Use new FD and DVARs calculations from nipype (`172 <https://github.com/nipreps/mriqc/pull/172>`__)
* ENH: Started with python3 compatibility
* ENH: Added new M2WM measure 158
* FIX: QI2 is skipped if background intensity is not appropriate (`147 <https://github.com/nipreps/mriqc/pull/147>`__)

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* FIX: Error inverting the T1w-to-MNI warping (`146 <https://github.com/nipreps/mriqc/pull/146>`__)
* FIX: TypeError computing DVARS (`145 <https://github.com/nipreps/mriqc/pull/145>`__)
* ENH: Plot figure of fitted background chi for QI2 (`143 <https://github.com/nipreps/mriqc/pull/143>`__)
* ENH: Move skull-stripping and reorient to NIworkflows (`142 <https://github.com/nipreps/mriqc/pull/142>`__)
* FIX: mriqc crashes if no anatomical scans are found (`141 <https://github.com/nipreps/mriqc/pull/141>`__)
* DOC: Added acknowledgments to CPAC team members (`134 <https://github.com/nipreps/mriqc/pull/134>`__)
* ENH: Use absolute imports (`133 <https://github.com/nipreps/mriqc/pull/133>`__)
* FIX: VisibleDeprecationWarning (`132 <https://github.com/nipreps/mriqc/pull/132>`__)
* ENH: Provide full FD/DVARS files (`128 <https://github.com/nipreps/mriqc/pull/128>`__)
* ENH: Use MCFLIRT to compute motion parameters. AFNI's 3dvolreg now is optional (`121 <https://github.com/nipreps/mriqc/pull/121>`__)
* FIX: BIDS trees with anatomical images with different acquisition tokens (`116 <https://github.com/nipreps/mriqc/pull/116>`__)
* FIX: BIDS trees with anatomical images with several runs (`112 <https://github.com/nipreps/mriqc/pull/112>`__)
* ENH: Options for ANTs normalization: reduced test times (`124 <https://github.com/nipreps/mriqc/pull/124>`__),
and updated options (`115 <https://github.com/nipreps/mriqc/pull/115>`__)

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* ENH: PDF reports now use RST templates and jinja2 (`109 <https://github.com/nipreps/mriqc/pull/109>`__)
* FIX: Single-session-multiple-run anatomical files were not correctly located (`112 <https://github.com/nipreps/mriqc/pull/112>`__)

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* DOC: Added examples of the PDF reports (`107 <https://github.com/nipreps/mriqc/pull/107>`__)
* FIX: Fixed problems with Python 3 when generating reports.

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* ENH: Python 3 compatibility (`99 <https://github.com/nipreps/mriqc/pull/99>`__)
* ENH: Add JSON settings file for ANTS (`95 <https://github.com/nipreps/mriqc/pull/95>`__)
* ENH: Generate reports automatically if mriqc is run without the -S flag (`93 <https://github.com/nipreps/mriqc/pull/93>`__)
* FIX: Revised implementation of QI2 measure (`90 <https://github.com/nipreps/mriqc/pull/90>`__)
* AGAVE: Fixed docker image for agave (`89 <https://github.com/nipreps/mriqc/pull/89>`__)
* FIX: Problem when generating the air mask with dipy installed (`88 <https://github.com/nipreps/mriqc/pull/88>`__)
* ENH: One-session-one-run execution mode (`85 <https://github.com/nipreps/mriqc/pull/85>`__)
* AGAVE: Added an agave app description generator (`84 <https://github.com/nipreps/mriqc/pull/84>`__)

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* ENH: Updated CircleCI and Docker to use the version 2.1.0 of ANTs
compiled by their developers.
* ENH: New anatomical workflows to compute the air mask (`56 <https://github.com/nipreps/mriqc/pull/56>`__)