1.2.5 (December 4, 2018)

Hotfix release.

[FIX] Breadcrumb reporting (#1435) @chrisfilo

1.2.4 (December 3, 2018)

Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates (with thanks to @emdupre).

[ENH] Update ME-EPI workflow to create optimal combination (#1263) @emdupre
[MAINT] Merge master into multiecho (#1324) @effigies
[ENH] Add echo-idx flag (#1355) @emdupre
[FIX] Always run FreeSurfer interfaces that sink outside working directory (#1397) @effigies
[ENH] Use Python 3.7 in Dockerfile (#1398) @effigies
[DOC] Update contributing guide and add code of conduct (#1404) @emdupre
[FIX] Calculate template transforms explicitly as RAS2RAS (#1399) @effigies
[MAINT] Replace img.get_affine() -> img.affine (#1414) @oesteban
[FIX] Truncating of sentry messages (#1417) @chrisfilo
[ENH] Add fmriprep-docker execution environment (#1416) @chrisfilo
[MAINT] Update indexed_gzip to handle small .nii.gz (#1421) @effigies
[ENH] Group common issues with fingerprints (#1418) @chrisfilo
[ENH] adding memory and cpu info to sentry logs (#1420) @chrisfilo
[ENH] Use standard T2* map as coregistration target (#1383) @emdupre
[ENH] Handle FreeSurfer subject directory preparation gracefully when run in parallel (#1413) @effigies
[ENH] Make sure inputs are BIDS compliant before running fmriprep (#1419) @chrisfilo
[ENH] Sentry event categorization propagation (#1422) @chrisfilo
[MAINT] Require nipype >= 1.1.6 (#1426) @effigies
[ENH] Omnibus multi-echo pull request (#1296) @effigies
[ENH] Report memory overcommit policies (#1429) @effigies

1.2.3 (November 16, 2018)

Refactor of Sentry reporting, bug fixes and added tests. With thanks to @sebnaze for contributions.

[TEST] Utility functions for skipping/re-inserting non-steady-state volumes (#1382) @jdkent
[FIX] Correctly populate right-hemisphere time series in CIFTI derivatives (#1378) @sebnaze
[FIX] Restore original contour colors in reports (#1385) @oesteban
[ENH] New sentry SDK (#1381) @chrisfilo
[ENH] Sentry refinement (#1394) @chrisfilo

1.2.2 (November 9, 2018)

Several bug fixes. With thanks to Franz Liem, Nir Jacoby and Markus Handal Sneve for contributions.

[FIX] Do not show --debug deprecation warning unless used (#1361) @effigies
[FIX] Select consistent parcellation for producing aparcaseg derivatives (#1369) @nirjacoby
[FIX] Count non-steady-state volumes even if sbref is passed (#1373) @effigies
[ENH] Respect SliceEncodingDirection metadata (#1350) @fliem
[ENH] Set maximum MELODIC components to 200 by default (#1366) @markushs
[TEST] Verify LegacyMultiProc functionality (#1368) @effigies

1.2.1 (November 1, 2018)

Hotfix release (deployment system)

1.2.0 (October 31, 2018)

This release marks a substantial renaming of derivatives to conform to the BIDS Derivatives specification [release candidate](https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI/).

The most significant additional change is a substantial revision of BOLD skull-stripping, using a BOLD template constructed from many open datasets. Building off the work of Zhifang Ye (see #1050), the skull-stripping is now much more resilient to intensity inhomogeneity.

With many thanks to Ali Cohen, James Kent, Inge Amlien, Sebastian Urchs, and Zhifang Ye for contributions.

[FIX] Missing BOLD reports (#1326) @oesteban
[FIX] Ensure encoding when reading boilerplate (#1322) @alioco
[FIX] Reportlets - bbregister vs flirtbbr (continues #1326) (#1328) @oesteban
[FIX] Quick update to new template structure (#1330) @oesteban
[FIX] Explicitly pass bold mask to AROMA (#1332) @jdkent
[FIX] Missing report output - #1339 (#1346) @kasbohm
[FIX] Remove non-steady-state volumes prior to ICA-AROMA (#1335) @jdkent
[ENH] Store BOLD reference images (#1306) @oesteban
[ENH] Deprecate --debug with --sloppy (#1347) @effigies
[ENH] Conform confound regressor names to Derivatives RC2 (#1343) @effigies
[ENH] Do not set KEEP_FILE_OPEN_DEFAULT (#1356) @effigies
[ENH] Template-based masking of EPI boldrefs (#1321) @oesteban
[DOC] Update BIDS-validator link (#1320) @surchs
[DOC] add --bind method to singularity patch documentation (#1340) @jdkent
[RF] Update anatomical derivatives for RC1 (#1325) @effigies
[RF] Update functional derivatives for RC1 (#1333) @effigies
[TST] Add heavily-nonuniform boldrefs for regression tests (#1329) @oesteban
[TST] Fix expectations for CIFTI outputs & ds005 (#1344) @oesteban
[MAINT] Ignore project settings files from popular python/code editors (#1336) @jdkent
[CI] Deploy poldracklab/fmriprep:unstable tracking master (#1307) @effigies

1.1.8 (October 4, 2018)

Several bug fixes. This release is intended to be the last before start adopting BIDS-Derivatives RC1 (which will trigger 1.2.x versions).

[DOC] Switch to orig graph for init_bold_t2s_wf (#1298) @effigies
[FIX] Enhance T2 contrast enhance_t2 in reference estimate (#1299) @effigies
[FIX] Create template from one usable T1w image (#1305) @effigies
[MAINT] Pin grabbit and pybids in setup.py (#1284) @oesteban

1.1.7 (September 25, 2018)

Several bug fixes. With thanks to Elizabeth Dupre and Romain Vala for contributions.

[FIX] Revert FreeSurfer download URL (#1280) @chrisfilo
[FIX] Default to 6 DoF for BOLD-T1w registration (#1286) @effigies
[FIX] Only grab sbref images, not metadata (#1285) @effigies
[FIX] QwarpPlusMinus renamed source_file to in_file (#1289) @effigies
[FIX] Remove long paths from all LTA output files (#1274) @romainVala
[ENH] Use single-band reference images when available (#1270) @effigies
[DOC] Note GIFTI surface alignment (#1288) @effigies
[REF] Split BOLD-T1w registration into calculation/application workflows (#1278) @emdupre
[MAINT] Pin pybids and grabbit in Docker build (#1281) @chrisfilo

1.1.6 (September 10, 2018)

Hotfix release.

[FIX] Typo in plugin config loading.

1.1.5 (September 06, 2018)

Improved documentation and minor bug fixes. With thanks to Jarod Roland and Taylor Salo for contributions.

[DOC] Replace --clearenv with correct --cleanenv flag (#1237) @jarodroland
[DOC] De-indent to remove text from code block (#1238) @effigies
[TST] Add enhance-and-skullstrip regression tests (#1074) @effigies
[DOC] Clearly indicate that fMRIPrep requires Python 3.5+ (#1249) @oesteban
[MAINT] Update PR template (#1239) @effigies
[DOC] Set appropriate version in Zenodo citation (#1250) @oesteban
[DOC] Updating long description (#1230) @oesteban
[DOC] Add ME workflow description (#1253) @tsalo
[FIX] Add memory annotation to ROIPlot interface (#1256) @jdkent
[ENH] Write derivatives dataset_description.json (#1247) @effigies
[DOC] Enable table text wrap and link docstrings to code on GitHub (#1258) @tsalo
[DOC] Clarify language describing T1w image merging (#1269) @chrisfilo
[FIX] Accommodate new template formats (#1273) @effigies
[FIX] Permit overriding plugin config with CLI options (#1272) @effigies

1.1.4 (August 06, 2018)

A hotfix release for #1235. Additionally, notebooks have been synced with the latest version of that repository.

[FIX] Verify first word of _cmd in dependency check (#1236)
[DOC] Add two missing references (#1234)
[ENH] Allow turning off random seeding for ANTs brain extraction (#919)

1.1.3 (July 30, 2018)

This release comes with many updates to the documentation, a more lightweight SignalExtraction, a new dynamic boilerplate and some new features from Nipype.

[ENH] Use upstream afni.TShift improvements (#1160)
[PIN] Nipype 1.1.1 (65078c9)
[ENH] Dynamic citation boilerplate (#1024)
[ENH] Check Command Line dependencies before running (#1044)
[ENH] Reimplement SignalExtraction (#1170)
[DOC] Update copyright year to 2018 (#1224)
[ENH] Enable -u (docker user/userid) flag in wrapper (#1223)
[FIX] Corrects Dockerfile WORKDIR. (#1218)
[ENH] More specific errors for missing echo times (#1221)
[ENH] Change WORKDIR of Docker image (#1204)
[DOC] Update documentation related to contributions (#1187)
[DOC] Additions to include before responding to reviews of the pre-print (#1195)
[DOC] Improving documentation on using Singularity (#1063)
[DOC] Add OHBM 2018 poster, presentation (#1198)
[ENH] Replace InvertT1w with upstream Rescale(invert=True) (#1161)

1.1.2 (July 6, 2018)

This release incorporates Nipype improvements that should reduce the chance of hanging if tasks are killed for excessive resource consumption.

Thanks to Elizabeth DuPre for documentation updates.

[DOC] Clarify how to reuse FreeSurfer derivatives (#1189)
[DOC] Improve command line option documentation (#1186, #1080)
[MAINT] Update core dependencies (#1179, #1180)

1.1.1 (June 7, 2018)

[ENH] Pre-cache DKT31 template in Docker image (#1159)
[MAINT] Update core dependencies (#1163)

1.1.0 (June 4, 2018)

[ENH] Use Reorient interface included upstream in nipype (#1153)
[FIX] Refine BIDS queries to avoid indexing derivatives (#1141)
[DOC] Clarify outlier columns (#1138)
[PIN] Update to niworkflows 0.4.0 and nipype 1.0.4 (#1133)

1.0.15 (May 17, 2018)

[DOC] Add lesion masking during registration (#1113)
[FIX] Patch boldbuffer for ME (#1134)

1.0.14 (May 15, 2018)

With thanks to @ZhifangYe for contributions

[FIX] Non-invertible transforms bringing parcellation to BOLD (#1130)
[FIX] Bad connection for --medial-surface-nan option (#1128)

1.0.13 (May 11, 2018)

With thanks to @danlurie for the outstanding contribution of #1106

[ENH] Some nit picks on reports (#1123)
[ENH] Carpetplot + confounds plot (#1114)
[ENH] Add constrained cost-function masking to T1-MNI registration (#1106)
[FIX] Circular dependency (#1104)
[ENH] Set PYTHONNOUSERSITE in containers (#1103)

1.0.12 (May 03, 2018)

[MAINT] fmriprep-docker: Ensure data/output/work paths are absolute (#1089)
[ENH] Add usage tracking and centralized error reporting (#1088)
[FIX] Ensure one motion IC index is loaded as list (#1096)
[TST] Refactoring CircleCI setup (#1098)
[FIX] Compression in DataSinks (#1095)
[MAINT] fmriprep-docker: Support Python 2/3 without future or other helpers (#1082)
[MAINT] Update npm to 10.x (#1087)
[DOC] Prefer pre-print over Zenodo doi in boilerplate (#1086)
[DOC] Stylistic fix (`'template'`) (#1083)
[FIX] Run ICA-AROMA in MNI152Lin 2mm resampling grid (91x109x91 vox) (#1064)
[MAINT] Remove cwebp to revert to png (#1081)
[ENH] Allow changing the dimensionality of Melodic for AROMA. (#1052)
[FIX] Derivatives datasink handling of compression (#1077)
[FIX] Check for invalid sform matrices (#1072)
[FIX] Check exit code from subprocess (#1073)
[DOC] Add preprint fig. 1 to About (#1070)
[FIX] Always strip session from T1w for derivative naming (#1071)
[DOC] Add RRIDs in the citation boilerplate (#1061)
[ENH] Generate CIFTI derivatives (#1001)

1.0.11 (April 16, 2018)

[FIX] Do not detrend CSF/WhiteMatter/GlobalSignal (#1058)

1.0.10 (April 16, 2018)

[TST] Re-run ds005 with only one BOLD run (#1048)
[FIX] Patch subject_summary in reports (#1047)

1.0.9 (April 10, 2018)

With thanks to @danlurie for contributions.

[FIX] Connect inputnode to SDC for pepolar images (#1046)
[FIX] Pass ref_file to STC check (#1038)
[DOC] Add BBR fallback to user docs. (#1036)
[ENH] Revise resampling grid for template outputs (#1040)
[MAINT] DataSinks within their workflows (#1021)
[ENH] Add FLAIR pial refinement support (#829)
[MAINT] Upgrade to pybids 0.5 (#1027)
[MAINT] Refactor fieldmap heuristics (#1017)
[FIX] Use metadata to select shortest echo as ref_file (#1018)
[ENH] Adopt versioneer to compose version names (#1007)
[ENH] Handle first echo separately for ME-EPI (#891)

1.0.8 (February 22, 2018)

With thanks to @mgxd and @naveau for contributions.

[FIX] ROIs Plot and output brain masks consistency (#1002)
[FIX] Init flirt with qform (#1003)
[DOC] Prepopulate tag when posting neurostars questions. (#987)
[FIX] Update fmap.py : import _get_pe_index in get_ees (#984)
[FIX] Argparse action (#985)

1.0.7 (February 13, 2018)

[ENH] Output aseg and aparc in T1w and BOLD spaces (#957)
[FIX] Write latest BOLD mask out (space-T1w) (#978)
[PIN] Updating niworkflows to 0.3.1 (#962)
[FIX] Robuster BOLD mask (#966)

1.0.6 (29th of January 2018)

[FIX] Bad connection in phasediff-fieldmap workflow (#950)
[PIN] niworkflows-0.3.1-dev (including Nipype 1.0.0!)
[ENH] Migrate to CircleCI 2.0 and workflows (#943)
[ENH] Improvements to CLIs (native & wrapper) (#944)
[FIX] Rerun tCompCor interface in case of MemoryError (#942)

1.0.5 (21st of January 2018)

[PIN] niworkflows-0.2.8 to fix several execution issues.
[ENH] Code cleanup (#938)

1.0.4 (15th of January 2018)

[FIX] Pin niworkflows-0.2.6 to fix several MultiProc errors (nipy/nipype#2368)
[DOC] Fix DOI in citation boilerplate (#933)
[FIX] Heuristics to prevent memory errors during aCompCor (#930).
[FIX] RuntimeWarning: divide by zero encountered in float_scalars (#931).
[FIX] INU correction before merging several T1w (#925).

1.0.3 (3rd of January 2018)

[FIX] Pin niworkflows-0.2.4 to fix (#868).
[FIX] Roll back run/task groupings after BIDS query (#918). Groupings for the multi-echo extension will be reenabled soon.

1.0.2 (2nd of January 2018)

[FIX] Grouping runs broke FMRIPREP on some datasets (#916) Thanks to @emdupre

1.0.1 (1st of January 2018)

With thanks to @emdupre for contributions.

[PIN] Update required niworkflows version to 0.2.3
[FIX] Refine antsBrainExtraction if recon-all is run (#912) With thanks to Arno Klein for his [helpful comments here](https://github.com/poldracklab/fmriprep/issues/431#issuecomment-299583391)
[FIX] Use thinner contours in reportlets (#910)
[FIX] Robuster EPI mask (#911)
[FIX] Set workflow return value before potential error (#887)
[DOC] Documentation about FreeSurfer and --fs-no-reconall (#894)
[DOC] Fix example in installation ants-nthreads -> omp-nthreads (#885) With thanks to @mvdoc.
[ENH] Allow for multiecho data (#875)

1.0.0 (6th of December 2017)

[ENH] Add --resource-monitor flag (#883)
[FIX] Collision between Multi-T1w and --no-freesurfer (#880)
[FIX] Setting use_compression on resampling workflows (#882)
[ENH] Estimate motion parameters before STC (#876)
[ENH] Add --stop-on-first-crash option (#865)
[FIX] Correctly handling xforms (#874)
[FIX] Combined ROI reportlets (#872)
[ENH] Strip reportlets out of full report (#867)

1.0.0-rc13 (1st of December 2017)

[FIX] Broken --fs-license-file argument (#869)

1.0.0-rc12 (29th of November 2017)

[ENH] Use Nipype MultiProc even for sequential execution (#856)
[REF] More memory annotations and considerations (#816)
[FIX] Controlling memory explosion (#854)
[WRAPPER] Mount nipype repositories as niworkflows submodule (#834)
[FIX] Reduce image loads in local memory (#839)
[ENH] Always sync qforms, refactor error messaging (#851)

1.0.0-rc11 (24th of November 2017)

[ENH] Check for invalid qforms in validation (#847)
[FIX] Update pybids to include latest bugfixes (#838)
[FIX] MultiApplyTransforms failed with nthreads=1 (#835)

1.0.0-rc10 (9th of November 2017)

[FIX] Adopt new FreeSurfer (v6.0.1) license mechanism (#787)
[ENH] Output affine transforms from original T1w images to preprocessed anatomical (#726)
[FIX] Correct headers in AFNI-generated NIfTI files (#818)
[FIX] Normalize T1w image qform/sform matrices (#820)

1.0.0-rc9 (2nd of November 2017)

[FIX] Fixed #776 (aCompCor - numpy.linalg.linalg.LinAlgError: SVD did not converge) via #807.
[ENH] Added CSF column to _confounds.tsv (included in #807)
[DOC] Add more details on the outputs of FMRIPREP and minor fixes (#811)
[ENH] Processing confounds in BOLD space (#807)
[ENH] Updated niworkflows and nipype, including the new feature to close all file descriptors (#810)
[REF] Refactored BOLD workflows module (#805)
[ENH] Improved memory annotations (#803, #807)

1.0.0-rc8 (27th of October 2017)

[FIX] Allow missing magnitude2 in phasediff-type fieldmaps (#802)
[FIX] Lower tolerance deciding t1_merge shapes (#798)
[FIX] Be robust to 4D T1w images (#797)
[ENH] Resource annotations (#746)
[ENH] Use indexed_gzip with nibabel (#788)
[FIX] Reduce FoV of outputs in T1w space (#785)

1.0.0-rc7 (20th of October 2017)

[ENH] Update pinned version of nipype to latest master
[ENH] Added rX permissions to make life easier on Singularity users (#757)
[DOC] Citation boilerplate (#779)
[FIX] Patch to remove long filenames after mri_concatenate_lta (#778)
[FIX] Only use unbiased template with --longitudinal (#771)
[FIX] Use t1_2_fsnative registration when sampling to surface (#762)
[ENH] Remove --skull_strip_ants option (#761)
[DOC] Add reference to beginners guide (#763)

1.0.0-rc6 (11th of October 2017)

[ENH] Add inverse normalization transform (MNI -> T1w) to derivatives (#754)
[ENH] Fall back to initial registration if BBR fails (#694)
[FIX] Header and affine transform updates to resolve intermittent misalignments in reports (#743)
[FIX] Register FreeSurfer template to FMRIPREP template, handling pre-run FreeSurfer subjects more robustly, saving affine to derivatives (#733)
[ENH] Add OpenFMRI participant sampler command-line tool (#704)
[ENH] For SyN-SDC, assume phase-encoding direction of A-P unless specified L-R (#740, #744)
[ENH] Permit skull-stripping with NKI ANTs template (#729)
[ENH] Erode aCompCor masks to target volume proportions, instead of fixed distances (#731, #732)
[DOC] Documentation updates (#748)

1.0.0-rc5 (25th of September 2017)

[FIX] Skip slice time correction on BOLD series < 5 volumes (#711)
[FIX] Skip AFNI check for new versions (#723)
[DOC] Documentation clarification and updates (#698, #711)

1.0.0-rc4 (12th of September 2017)

With thanks to Mathias Goncalves for contributions.

[ENH] Collapse ITK transforms of head-motion correction in only one file (#695)
[FIX] Raise error when run.py is called directly (#692)
[FIX] Parse crash files when they are stored as text (#690)
[ENH] Replace medial wall values with NaNs (#687)

1.0.0-rc3 (28th of August 2017)

With thanks to Anibal Sólon for contributions.

[ENH] Add --low-mem option to reduce memory usage for large BOLD series (#663)
[ENH] Parallelize anatomical conformation step (#666)
[FIX] Handle missing functional data in SubjectSummary node (#670)
[FIX] Disable --no-skull-strip-ants (AFNI skull-stripping) (#674)
[FIX] Initialize SyN SDC more robustly (#680)
[DOC] Add comprehensive documentation of workflow API (#638)

1.0.0-rc2 (12th of August 2017)

[ENH] Increased support for partial field-of-view BOLD datasets (#659)
[FIX] Slice time correction is now being applied to output data (not only to intermediate file used for motion estimation - #662)
[FIX] Fieldmap unwarping is now being applied to MNI space outputs (not only to T1w space outputs - #662)

1.0.0-rc1 (8th of August 2017)

[ENH] Include ICA-AROMA confounds in report (#646)
[ENH] Save non-aggressively denoised BOLD series (#648)
[ENH] Improved logging messages (#621)
[ENH] Improved resource management (#622, #629, #640, #641)
[ENH] Improved confound header names (#634)
[FIX] Ensure multi-T1w image datasets have RAS-oriented template (#637)
[FIX] More informative errors for conflicting options (#632)
[DOC] Improved report summaries (#647)

0.6.0 (31st of July 2017)

With thanks to Yaroslav Halchenko and Ilkay Isik for contributions.

[ENH] Set threshold on up-sampling ratio in conformation, report results (#601)
[ENH] Censor non-steady-state volumes prior to CompCor (#603)
[FIX] Conformation failure in thick-slice, oblique T1w datasets (#601)
[FIX] Crash/report failure of phase-difference SDC pipeline (#602, #604)
[FIX] Prevent AFNI NIfTI extensions from crashing reference EPI estimation (#619)
[DOC] Save logs to output directory (#605)
[ENH] Upgrade to ICA-AROMA 0.4.1-beta (#611)

0.5.4 (20th of July 2017)

[DOC] Improved report summaries describing steps taken (#584)
[ENH] Uniformize command-line argument style (#592)

0.5.3 (18th of July 2017)

With thanks to Yaroslav Halchenko for contributions.

[ENH] High-pass filter time series prior to CompCor (#577)
[ENH] Validate and minimally conform BOLD images (#581)
[FIX] Bug that prevented PE direction estimation (#586)
[DOC] Log version/time in report (#587)

0.5.2 (30th of June 2017)

With thanks to James Kent for contributions.

[ENH] Calculate noise components in functional data with ICA-AROMA (#539)
[FIX] Remove unused parameters from function node, resolving crash (#576)

0.5.1 (24th of June 2017)

[FIX] Invalid parameter in bbreg_wf (#572)

0.5.0 (21st of June 2017)