Mriqc

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* ENH: Add mriqc version and input image hash to IQMs json file (`432 <https://github.com/nipreps/mriqc/pull/432>`__)
* FIX: Affine and warp transforms are now applied in the correct order (`431 <https://github.com/nipreps/mriqc/pull/431>`__)

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* FIX: BOLD reports clipped IQMs after spikes_num (`425 <https://github.com/nipreps/mriqc/pull/425>`__)
* FIX: Unicode error writing group reports (`424 <https://github.com/nipreps/mriqc/pull/424>`__)
* FIX: Respect Nifi header in fMRI conform node (`415 <https://github.com/nipreps/mriqc/pull/415>`__)
* DOC: Deep revision of documentation (411, 416)
* ENH: Added sphinx extension to plot workflow graphs (`411 <https://github.com/nipreps/mriqc/pull/411>`__)
* FIX: Removed repeated bias correction on anatomical workflows (`410 <https://github.com/nipreps/mriqc/pull/410>`__)
* FIX: Race condition in bold workflow when using shared workdir (`409 <https://github.com/nipreps/mriqc/pull/409>`__)
* FIX: Tests (408, 407, 405)
* FIX: Remove CDN for group level reports (`406 <https://github.com/nipreps/mriqc/pull/406>`__)
* FIX: Unused connection, matplotlib segfault (403, 402)
* ENH: Skip SpikeFFT detector by default (`400 <https://github.com/nipreps/mriqc/pull/400>`__)
* ENH: Use float32 (`399 <https://github.com/nipreps/mriqc/pull/399>`__)
* ENH: Spike finder performance improvoments (`398 <https://github.com/nipreps/mriqc/pull/398>`__)
* ENH: Basic T2w workflow (`394 <https://github.com/nipreps/mriqc/pull/394>`__)
* ENH: Re-enable 3dvolreg (`390 <https://github.com/nipreps/mriqc/pull/390>`__)
* ENH: Add T1w classifier (`389 <https://github.com/nipreps/mriqc/pull/389>`__)

---------------

* FIX: Remove non-repeatable step from pipeline (`369 <https://github.com/nipreps/mriqc/pull/369>`__)
* ENH: Improve group level command line, with more informative output when no IQMs are found for a modality (`372 <https://github.com/nipreps/mriqc/pull/372>`__)
* ENH: Make group reports self-contained (`333 <https://github.com/nipreps/mriqc/pull/333>`__)
* FIX: New mosaics, based on old ones (361, 360, 334)
* FIX: Require numpy>=1.12 to avoid casting problems (`356 <https://github.com/nipreps/mriqc/pull/356>`__)
* FIX: Add support for acq and rec tags of BIDS (`346 <https://github.com/nipreps/mriqc/pull/346>`__)
* DOC: Documentation updates (`350 <https://github.com/nipreps/mriqc/pull/350>`__)
* FIX: pybids compatibility "No scans were found" (340, 347, 342)
* ENH: Rewrite PYTHONPATH in docker/singularity images (`345 <https://github.com/nipreps/mriqc/pull/345>`__)
* ENH: Move metadata onto the bottom of the individual reports (`332 <https://github.com/nipreps/mriqc/pull/332>`__)
* ENH: Don't include MNI registration report unlesS --verbose-reports is used (`362 <https://github.com/nipreps/mriqc/pull/362>`__)

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* ENH: Added registration svg panel to reports (`297 <https://github.com/nipreps/mriqc/pull/297>`__)

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* FIX: Bug translating int16 to uint8 in conform image.
* FIX: Error in ConformImage interface (`297 <https://github.com/nipreps/mriqc/pull/297>`__)
* ENH: Replace BBR by ANTs (295, 296)
* FIX: Singularity: user-environment leaking into container (`293 <https://github.com/nipreps/mriqc/pull/293>`__)
* ENH: Report failed cases in group report (`291 <https://github.com/nipreps/mriqc/pull/291>`__)
* FIX: Brighter anatomical --verbose-reports (`290 <https://github.com/nipreps/mriqc/pull/290>`__)
* FIX: X-flip in the mosaics (`289 <https://github.com/nipreps/mriqc/pull/289>`__)
* ENH: Show metadata in the individual report (`288 <https://github.com/nipreps/mriqc/pull/288>`__)
* ENH: Label in the cutoff threshold - fmriplot (`287 <https://github.com/nipreps/mriqc/pull/287>`__)
* ENH: PyBIDS (`286 <https://github.com/nipreps/mriqc/pull/286>`__)
* ENH: Simplify tests (`284 <https://github.com/nipreps/mriqc/pull/284>`__)
* FIX: MRIQC crashed generating csv files (`283 <https://github.com/nipreps/mriqc/pull/283>`__)
* FIX: Bug in setup.py (`281 <https://github.com/nipreps/mriqc/pull/281>`__)
* ENH: Makefile (`280 <https://github.com/nipreps/mriqc/pull/280>`__)
* FIX: Revision of IQMs (266, 272, 279)
* ENH: Deprecation of --nthreads, new flags (`260 <https://github.com/nipreps/mriqc/pull/260>`__)
* ENH: Improvements on plots rendering (254, 257, 258, 267, 268, 269, 270)
* ENH: FFT detection of spikes (253, 272)
* FIX: Labels and links of samples in group plots (`249 <https://github.com/nipreps/mriqc/pull/249>`__)
* ENH: Units in group plots (`242 <https://github.com/nipreps/mriqc/pull/242>`__)
* FIX: More reliable group level (`238 <https://github.com/nipreps/mriqc/pull/238>`__)
* ENH: Add --verbose-reports for fMRI (`236 <https://github.com/nipreps/mriqc/pull/236>`__)
* ENH: Migrate functional reports to html (`232 <https://github.com/nipreps/mriqc/pull/232>`__)
* ENH: Add 0.2 FD cutoff line (`231 <https://github.com/nipreps/mriqc/pull/231>`__)
* ENH: Add AFNI's outlier count to carpet plot confound charts (`230 <https://github.com/nipreps/mriqc/pull/230>`__)

-------------

* ENH: Anatomical Group reports in html (`227 <https://github.com/nipreps/mriqc/pull/227>`__)
* ENH: Add kurtosis to summary statistics (`224 <https://github.com/nipreps/mriqc/pull/224>`__)
* ENH: New report layout for fMRI, added carpetplot (`198 <https://github.com/nipreps/mriqc/pull/198>`__)
* ENH: Anatomical workflow refactor (`219 <https://github.com/nipreps/mriqc/pull/219>`__).