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CHANGES.txt
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CHANGES.txt
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* [ENH] Second revision of the classifier (#555):
* Set matplotlib plugin to `agg` in docker image
* Migrate scalings to sklearn pipelining system
* Add Satra's feature selection for RFC
* Make model selection compatible with sklearn `Pipeline`
* Multiclass classification
* Add feature selection filter based on Sites prediction (requires pinning to development sklearn-0.19)
* Add `RobustLeavePGroupsOut`, replace `RobustGridSearchCV` with the standard `GridSearchCV` of sklearn.
* Choice between `RepeatedStratifiedKFold` and `RobustLeavePGroupsOut` in `mriqc_clf`
* Write cross-validation results to an `.npz` file.
* [ENH] First revision of the classifier (#553):
* Add the possibility of changing the scorer function.
* Unifize labels for raters in data tables (to `rater_1`)
* Add the possibility of setting a custom decision threshold
* Write the probabilities in the prediction file
* Revised `mriqc_clf` processing flow
* Revised labels file for ds030.
* Add IQMs for ABIDE and DS030 calculated with MRIQC 0.9.6.
* ANNOUNCEMENT: Dropped support for Python<=3.4
0.9.6
=====
* [ENH] Finished setting up `MRIQC Web API <https://mriqc.nimh.nih.gov>`_
* [ENH] Better error message when --participant_label is set (#542)
* [FIX] Allow --load-classifier option to be empty in mriqc_clf (#544)
* [FIX] Borked bias estimation derived from Conform (#541)
* [ENH] Test against web API 0.3.2 (#540)
* [ENH] Change the default Web API address (#539)
* [ENH] MRIQCWebAPI: hash fields that may have PI (#538)
* [ENH] Added token authorization to MRIQCWebAPI client (#535)
* [FIX] Do not mask and antsAffineInitializer twice (#534)
* [FIX] Datasets where air (hat) mask is empty (#533)
* [ENH] Integration testing for MRIQCWebAPI (#520)
* [ENH] Use AFNI to calculate gcor (#531)
* [ENH] Refactor derivatives (#530)
* [ENH] New bold-IQM: dummy_trs (non-stady state volumes) (#524)
* [FIX] Order of BIDS components in IQMs CSV table (#525)
* [ENH] Improved logging of mriqc_run (#526)
0.9.5
=====
* [ENH] Refactored structural metrics calculation (#513)
* [ENH] Calculate rotation mask (#515)
* [ENH] Intensity harmonization in the anatomical workflow (#510)
* [ENH] Set N4BiasFieldCorrection number of threads (#506)
* [ENH] Convert FWHM in pixel units (#503)
* [ENH] Add MRIQC client for feature crowdsourcing (#464)
* [DOC] Fix functional feature labels in documentation (docs_only) (#507)
* [FIX] New implementation for the rPVE feature (normalization, left-tail values) (#505)
* [ENH] Parse BIDS selectors (run, task, etc.), improve CLI (#504)
0.9.4
=====
* ANNOUNCEMENT: Dropped Python 2 support
* [ENH] Use versioneer to handle versions (#500)
* [ENH] Speed up spatial normalization (#495)
* [ENH] Resampling of hat mask and TPMs with linear interp (#498)
* [TST] Build documentation in CircleCI (#484)
* [ENH] Use full-resolution T1w images from ABIDE (#486)
* [TST] Parallelize tests (#493)
* [TST] Binding /etc/localtime stopped working in docker 1.9.1 (#492)
* [TST] Downgrade docker to 1.9.1 in circle (build_only) (#491)
* [TST] Check for changes in intermediate nifti files (#485)
* [FIX] Erroneous flag --n_proc in CircleCI (#490)
* [ENH] Add build_only tag to circle builds (#488)
* [ENH] Update Dockerfile (#482)
* [FIX] Ignore --profile flag with Linear plugin (#483)
* [DOC] Deep revision of the documentation (#479)
* [ENH] Minor improvements: SpatialNormalization and segmentation (#472)
* [ENH] Fixed typo for neurodebian install via apt-get (#478)
* [ENH] Updating fs2gif script (#465)
* [ENH] RF: Use niworkflows.interface.SimpleInterface (#468)
* [ENH] Add reproducibility of metrics tracking (#466)
Release 0.9.3
=============
* [ENH] Reafactor of the Dockerfile to improve transparency, reduce size, and enable injecting code in Singularity (#457)
* [ENH] Make more the memory consumption estimates of each processing step more conservative to improve robustness (#456)
* [FIX] Minor documentation cleanups (#461)
Release 0.9.2
=============
* [ENH] Optional ICA reports for identifying spatiotemporal artifacts (#412)
* [ENH] Add --profile flag (#435)
* [ENH] Crashfiles are saved in plain text to improve portability (#434)
* [FIX] Fixes EPI mask erosion (#442)
* [ENH] Make FSL and AFNI motion correction more comparable by using the same scheme for defining the reference image (#444)
* [FIX] Temporarily disabling T1w quality classifier until it can be retrained on new measures (#447)
Release 0.9.1
=============
* [ENH] Add mriqc version and input image hash to IQMs json file (#432)
* [FIX] Affine and warp transforms are now applied in the correct order (#431)
Release 0.9.0-2
===============
* [ENH] Revise Docker paths (#429)
* [FIX] Greedy participant selection (#426)
* [FIX] Pin pybids to new version 0.1.0 (#427)
* [FIX] Amends sloppy PR #425 (#428)
Release 0.9.0-1
===============
* [FIX] BOLD reports clipped IQMs after spikes_num (#425)
* [FIX] Unicode error writing group reports (#424)
* [FIX] Respect Nifi header in fMRI conform node (#415)
* [DOC] Deep revision of documentation (#411, #416)
* [ENH] Added sphinx extension to plot workflow graphs (#411)
* [FIX] Removed repeated bias correction on anatomical workflows (#410)
* [FIX] Race condition in bold workflow when using shared workdir (#409)
* [FIX] Tests (#408, #407, #405)
* [FIX] Remove CDN for group level reports (#406)
* [FIX] Unused connection, matplotlib segfault (#403, #402)
* [ENH] Skip SpikeFFT detector by default (#400)
* [ENH] Use float32 (#399)
* [ENH] Spike finder performance improvoments (#398)
* [ENH] Basic T2w workflow (#394)
* [ENH] Re-enable 3dvolreg (#390)
* [ENH] Add T1w classifier (#389)
Release 0.9.0-0
===============
* [FIX] Remove non-repeatable step from pipeline (#369)
* [ENH] Improve group level command line, with more informative output when no IQMs are found for a modality (#372)
* [ENH] Make group reports self-contained (#333)
* [FIX] New mosaics, based on old ones (#361, #360, #334)
* [FIX] Require numpy>=1.12 to avoid casting problems (#356)
* [FIX] Add support for acq and rec tags of BIDS (#346)
* [DOC] Documentation updates (#350)
* [FIX] pybids compatibility "No scans were found" (#340, #347, #342)
* [ENH] Rewrite PYTHONPATH in docker/singularity images (#345)
* [ENH] Move metadata onto the bottom of the individual reports (#332)
* [ENH] Don't include MNI registration report unlesS --verbose-reports is used (#362)
Release 0.8.9
=============
* [ENH] Added registration svg panel to reports (#297)
Release 0.8.8
=============
* [FIX] Bug translating int16 to uint8 in conform image.
* [FIX] Error in ConformImage interface (#297)
* [ENH] Replace BBR by ANTs (#295, #296)
* [FIX] Singularity: user-environment leaking into container (#293)
* [ENH] Report failed cases in group report (#291)
* [FIX] Brighter anatomical --verbose-reports (#290)
* [FIX] X-flip in the mosaics (#289)
* [ENH] Show metadata in the individual report (#288)
* [ENH] Label in the cutoff threshold - fmriplot (#287)
* [ENH] PyBIDS (#286)
* [ENH] Simplify tests (#284)
* [FIX] MRIQC crashed generating csv files (#283)
* [FIX] Bug in setup.py (#281)
* [ENH] Makefile (#280)
* [FIX] Revision of IQMs (#266, #272, #279)
* [ENH] Deprecation of --nthreads, new flags (#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)
* [ENH] Units in group plots (#242)
* [FIX] More reliable group level (#238)
* [ENH] Add --verbose-reports for fMRI (#236)
* [ENH] Migrate functional reports to html (#232)
* [ENH] Add 0.2 FD cutoff line (#231)
* [ENH] Add AFNI's outlier count to carpet plot confound charts (#230)
Release 0.8.7
=============
* [ENH] Anatomical Group reports in html (#227)
* [ENH] Add kurtosis to summary statistics (#224)
* [ENH] New report layout for fMRI, added carpetplot (#198)
* [ENH] Anatomical workflow refactor (#219).
Release 0.8.6
=============
* [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)
* [ENH] Started with python3 compatibility
* [ENH] Added new M2WM measure #158
* [FIX] QI2 is skipped if background intensity is not appropriate (#147)
Release 0.8.5
=============
* [FIX] Error inverting the T1w-to-MNI warping (#146)
* [FIX] TypeError computing DVARS (#145)
* [ENH] Plot figure of fitted background chi for QI2 (#143)
* [ENH] Move skull-stripping and reorient to NIworkflows (#142)
* [FIX] mriqc crashes if no anatomical scans are found (#141)
* [DOC] Added acknowledgments to CPAC team members (#134)
* [ENH] Use absolute imports (#133)
* [FIX] VisibleDeprecationWarning (#132)
* [ENH] Provide full FD/DVARS files (#128)
* [ENH] Use MCFLIRT to compute motion parameters. AFNI's 3dvolreg now is optional (#121)
* [FIX] BIDS trees with anatomical images with different acquisition tokens (#116)
* [FIX] BIDS trees with anatomical images with several runs (#112)
* [ENH] Options for ANTs normalization: reduced test times (#124),
and updated options (#115)
Release 0.8.4
=============
* [ENH] PDF reports now use RST templates and jinja2 (#109)
* [FIX] Single-session-multiple-run anatomical files were not correctly located (#112)
Release 0.8.3
=============
* [DOC] Added examples of the PDF reports (#107)
* [FIX] Fixed problems with Python 3 when generating reports.
Release 0.8.2
=============
* [ENH] Python 3 compatibility (#99)
* [ENH] Add JSON settings file for ANTS (#95)
* [ENH] Generate reports automatically if mriqc is run without the -S flag (#93)
* [FIX] Revised implementation of QI2 measure (#90)
* [AGAVE] Fixed docker image for agave (#89)
* [FIX] Problem when generating the air mask with dipy installed (#88)
* [ENH] One-session-one-run execution mode (#85)
* [AGAVE] Added an agave app description generator (#84)
Release 0.3.0
=============
* [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)
Release 0.2.0
=============
Release 0.1.0
=============
* [FIX] #55
* [ENH] Added rotation of output csv files if they exist
Release 0.0.2
=============
* [ENH] Completed migration from QAP
* [ENH] Integration with ReadTheDocs
* [ENH] Submission to PyPi
Release 0.0.1
=============
* Basic mriqc functionality