1.0.13

Release Notes

FMRIPrep-1.0.13 includes a major new feature with the addition of improved registration of atypical brains to the MNI template, by enabling cost-function masking. This is useful e.g. on brains with focal lesions.

With thanks to @danlurie for the outstanding contribution of this cool new feature.

CHANGES

• [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

Release Notes

A long overdue release. This release integrates the great work of @mgxd to provide results in the CIFTI/grayordinates format for surface-based analyses. It also fixes several issues related to ICA-AROMA, and a long list of miscellaneous improvements.

CHANGES

• [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

Release notes

Hotfix to the negative values within the global signals regressors (#1015).

CHANGES

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

1.0.10

Release Notes

Hotfix version to address https://neurostars.org/t/fmriprep-traiterror/1538

CHANGES

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

1.0.9

Release notes

Hotfix to a problem identified in the "PEPOLAR" susceptibility distortion correction path.

With thanks to @danlurie for contributions.

CHANGES

• [MAINT] Update pinning of niworkflows, nibabel, indexed_gzip and pybids.
• [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

Release notes

Minor bugfixes, niworkflows pinned to latest version 0.3.4.

CHANGES

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

Release notes

A release with several hotfixes, and the new feature of mapping FreeSurfer's aseg and aparc+aseg into subject space.

CHANGES

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

1.0.6-2

Testing deployment from CircleCI

1.0.6-1

Release to check new CircleCI deployment.

1.0.6

Release notes

This release addresses the major issues arisen from finishing Testing Phase 2 (see https://github.com/poldracklab/fmriprep/milestone/19) in combination with the very recent Nipype 1.0.0 release.

CHANGES

• [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)