New features and enhancements

• Upgrade to fMRIPrep 25.2.3 (#877)
• Add --bids-database-dir and --spec-file options for compatibility with Nipoppy (#879, #919)

Bug fixes

• Only resample atlases when needed (#874)
• Fix crash for zero-variance confounds regressors (#874)
• Fix new user interface crashes (#876, #878, #883, #886, #887, #889, #890, #892, #891, #894, #898, #899, #900, #901, #902, #910, #911, #905, #913, #915)

Maintenance

• Make more conda packages noarch packages (#873)
• Update mapca for compatibility with Nilearn (#874)
• Update README.rst to refer to latest released container (#893)
• Update consistency check code (#906, #918)

With many thanks to @F-Tomas, @lalalavi and @harveyaa for contributions

New features and enhancements

• Improvements to terminal-based user interface (#852, #853, #854, #861)

Bug fixes

• Fix ICA-AROMA component calculation (#870)
• Reduce memory usage for tSNR calculation (#863)
• Add memory usage prediction for additional nodes (#865)

New features and enhancements

• Upgrade to fMRIPrep 25.1.1 (#746, #791, #792, #797, #806, #819)
• Add new terminal-based user interface (#705, #795, #798, #802, #812, #814, #835, #838, #845, #848)
• Standardize confounds to reduce numerical errors in confounds regression (#785)
• Add unit tests to evaluate consistency of outputs across version (#803, #807)
• Support passing lesion masks and brain masks to fMRIPrep for preprocessing (#809, #844)
• Add option to calculate features in native space (#817, #850)
• Support single trial estimation with least-squares all and least-squares single (#830, #834)
• Add GIG-ICA feature to support NeuroMark (#828, #834)
• Make within-subject z-scoring of ReHo and fALFF optional (#832)

Bug fixes

• Fix loading TotalReadoutTime for field maps from BIDS metadata (#811)
• Fix spurious warning about missing slice timing metadata (#832)
• Add warning for when field maps are skipped due to missing metadata (#843)
• Fix passing units in the JSON sidecar for field map files (#846)

Maintenance

• Move container build to conda packages (#746, #792, #815, #826)
• Ensure compatibility with newer nipype (#801)

With many thanks to @lalalavi, @F-Tomas, @gjheij, @jstaph, Charlotte Meinke and Sarah Wellan for contributions

Bug fixes

• Backport fix for disabling tqdm in multiprocessing child processes

New features and enhancements

• Add motion scrubbing (#769)
• Add group-level command (#413, #416, #468, #477, #484, #496, #523, #543, #555, #556, #557, #558, #562, #566, #569,
  #574, #587, #589, #602, #604, #605, #612, #619, #621, #625, #635)
• Also remove empty directories when --keep none is enabled to reduce inode usage (#283)
• Add additional related images for the quality check (#295)
• Add import option to quality check (#328)
• Update documentation (#680, #748)
• Compatibility with COINSTAC (#322, #467)
• Additional unit tests (#338, #340, #384, #403, #421)
• Improve performance (#366, #646, #650, #651)
• Add sigmasquareds output for task-based features to allow Cohen's d calculation on the first level (#378)
• Better error messages for invalid metadata (#527)
• Add more comments to code (#665)

Bug fixes

• Fix handling of not a number values in stats (#319)
• Fix handling of additional errors in stats (#345)
• Fix handling of data with unknown BIDS tags (#244, #226, #337)
• Fix loading conditions from MAT files (#345)
• Fix reset of the global_settings in the spec.json file when adding a new feature (#345)
• Fix detecting unrealistic slice timing values (#342, #347)
• Fix handling of pre-computed fieldmaps (#348)
• Fix filtering out incomplete PEPOLAR field map sets (#370)
• Fix loading numerical condition names for TSV files (#370)
• Fix user interface crash when there are too many distinct tag values to fit on screen (#400, #493)
• Fix selecting Skip in the band pass filter setting (#498, #500)
• Fix handling of underscores in subject IDs (#499)
• Fix quality check inclusion decisions when aggregating multiple scans before group statistics (#490, #501)
• Fix handling of dummy scans to actually remove volumes from outputs (#506)
• Fix loading condition files in FSL 3-column format that do not have the extension .txt (#543)
• Fix handling of empty tag values (#549, #557)
• Fix accidental modification of database when searching dor condition files (#571)
• Fix detecting the orientation for unusual input files (#694, #706)
• Fix backspace key in user interface (#722)
• Fix spacing in user interface (#777)

Maintenance

• De-deduplicate code (#392, #411, #417)
• Fix code style (#451)
• Upgrade to Python 3.11 (#486)
• Use self-hosted runner for continuous integration (#554, #622)
• Add more type annotations (#599, #666)
• Use conda to install all dependencies (#701, #702, #741)
• Update ants version (#691)
• Update build script for creating singularity containers (#766)

With many thanks to @lalalavi, @F-Tomas, @dominikgoeller and @jstaph for contributions

Bug fixes

• Fix issue with BOLD to T1w registration (#230, #238, #239)
• Also detect exclude.json files that are placed in the reports/ folder (#228)
• Improve error message when the FreeSurfer license file is missing (#231)
• Fix a rare calculation error for fd_mean and related image quality metrics (#237, #241)
• Fix various warning messages (#247)
• Fix performance issue when collecting inputs for group statistics ()
• Fix a user interface issue where the option Start over after models was missing (#259, #260)
• Fix an issue where sub- prefixes were not recognized correctly when filtering inputs for group statistics (#264)
• Fix an issue when writing mixed data type columns to the text files in the reports/ folder (#274)
• Fix warnings for missing quality check information (#276)
• Fix errors when aggregating subjects with different numbers of scans during group statistics (#280)
• Fix error when fMRIPrep skips a BOLD file (#285)

Maintenance

• Bump indexed_gzip (#240)
• Bump nipype after bug fix (#255)
• Bump fmriprep after bug fix (#262)
• Upgrade to Python 3.10, clean up code and add more unit tests (#269)
• Make continuous integration tests run faster (#282, #284)
• Add type checking and linting to continuous integration (#285)

Bug fixes

• Fix issues that occurred after re-scaling fd_perc to be percent (#217)
• Catch error when NaN values occur within the linear algebra code (#215)
• Reduce memory usage when running large workflows by only loading the
  chunks that will be necessary for the current process (#216)
• Improve memory usage prediction for cluster submission scripts (#219)
• Update metadata module with better log messages (#220)

New features and enhancements

• Improve the assignment of field maps to functional scans, print
  warnings when detecting an incomplete field map or when a complete
  field map is not recognized by fMRIPrep (#115 and #192)
• Remove conditions that have no events from the task-based model. This
  is important for designs where the conditions depend on subject
  performance (#90)
• Output additional images during group mode. Voxel-wise descriptive
  statistics (#142), typical subject-level variance (#148)
• Divide outputs into subfolders to make navigating the files easier
• Output metadata to sidecar files, including resolution, field-of-view
  and field map type (#154 and #181)
• Add an option to skip dummy/non-steady-state scans and modify event
  onsets accordingly (#167, #176, #182 and #187)
• Improve performance during workflow creation (#192)

Bug fixes

• Update fMRIPrep to fix normalization bug (#51)
• Improve memory usage prediction. Fixes BrokenProcessPool and
  Killed: 137 errors (#125, #156 and #157)
• Refactor Dockerfile to correctly re-build matplotlib caches
  (#107)
• Fix assignment of event files to functional scans. Make sure that the
  assignment is consistent between what is shown in the user interface
  and during workflow creation. Add unit tests (#139)
• Fix crashes for datasets deviating from the BIDS specification
  and remove misleading warnings for incompatible and hidden files
• Fix AssertionError crash when no group model is specified
• Rephrase user interface for loading .mat event files. Do not say
  that the time unit (seconds or scans) is missing, which was
  confusing.
• Fix various crashes when running on a cluster
• Fix user interface crash when no categorical variables are defined in
  a spreadsheet
• Fix loading subject-level results during group model. Get rid of
  LoadResult nodes, instead use a subclass of Node (#137)
• Use slower but more robust least-squares solve for group statistics
  (#141)
• Fix performance issue during t2z_convert procedure during group
  statistics (#143, #144 and #145)
• Remove output from heterogeneity group statistics that was causing
  performance issues (#146)
• Fix confusing EOFError message on exit by gracefully stopping
  child processes before exit (#130 and #160)
• Fix running FreeSurfer with run_reconall option (#87)
• Add error message when running on an unsupported file system such as
  FAT (#102)
• Fix confusing error message when no features are specified (#147)
• Re-scale fd_perc output to percent (#186)
• Reduce user interface memory usage (#191)
• Fix automated testing hanging on the logging worker (#192)

Maintenance

• Update Python to version 3.8
• Update templateflow, pybids, nibabel
• Pin dipy version due to incompatibility with nipype
• Pin indexed_gzip version due to incompatibility of newer version
  with some files (#85)
• Add new Singularity container build workflow (#97 and #138)
• Improve documentation to suggest running Singularity with
  --containall instead of --no-home --cleanenv
• Refactor code to use defaultdict to increase readability
• Add more type hints
• Rename main branch from master to main
• Add pre-commit and pip-tools to better manage dependencies
• Install as many dependencies as possible via conda and the rest
  via pip (#164)
• Refactor workflow code to allow handling of surface-based functional
  images (#161)
• In-progress refactor model package into schema package. Use
  dataclasses for better integration with type checkers (#173, #174
  and #178)