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fMRIPrep 23.2.0alpha#3108

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effigies merged 181 commits intomasternipreps/fmriprep:masterfrom nextnipreps/fmriprep:nextCopy head branch name to clipboardNov 21, 2023

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Commits on Jan 19, 2023

• ENH: Upgrade FreeSurfer to 7.3.2

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• MNT: Try reducing FreeSurfer size by excluding large and test Python modules

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• DOCKER: Switch to conda for convert3d

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• DOCKER: Install libpng12 from PPA

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• DOC: Update versions in documentation

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• CI: Bump build cache

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• PIN: smriprep feature branch

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• CLI: Rename --anat-derivatives to --derivatives

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• RF: Collect pre-computed anatomical derivatives using new machinery

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• RF: Compute T1w-fsnative transform LTA from fsnative2t1w_xfm

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• WRAPPER: Update CLI arguments

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• CI: Update FASTRACK_ARG to use --derivatives

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• CI: Drop fasttrack output files; precomputed files are copied

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Commits on Jun 19, 2023

• MNT: Pin smriprep@next [skip ci]

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• Merge remote-tracking branch 'upstream/next' into rf/split_workflow

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Commits on Jun 20, 2023

• CI: Disable output checks, just show results

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Commits on Jul 4, 2023

• Merge remote-tracking branch 'upstream/master' into next

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• Merge remote-tracking branch 'upstream/next' into rf/split_workflow

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Commits on Jul 12, 2023

• MNT: Pin sdcflows feature branch

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Commits on Jul 19, 2023

• WIP: Refactor fit workflow

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Commits on Jul 20, 2023

• Draft to create the boldref for coregistration to T1w.

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Commits on Jul 21, 2023

• ENH: Add io spec for expected outputs from "fit" portion

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Commits on Jul 22, 2023

• Merge remote-tracking branch 'upstream/master' into next

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• Merge remote-tracking branches 'upstream/next', 'feilong/rf/split_workflow' and 'mgxd/rf/fit-io' into rf/split_workflow

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Commits on Jul 23, 2023

• Add -output-weights-text to -volume-to-surface-mapping

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• Revert "MNT: Pin sdcflows feature branch"

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Commits on Jul 30, 2023

• Merge remote-tracking branch 'HippocampusGirl/output-weights-text' into rf/split_workflow

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Commits on Aug 1, 2023

• Merge remote-tracking branch 'upstream/master' into next [skip ci]

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• Merge remote-tracking branch 'upstream/next' into rf/split_workflow

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Commits on Aug 9, 2023

• RF: Move fit workflow to workflows.bold.fit

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• RF: Add single subject fit workflow

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Commits on Aug 15, 2023

• FIX: Do not assume sbrefs

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• FIX: Correctly detect previous runs of fMRIPrep

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• FIX: Typos, logic errors, and unfinished refactors

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• ENH: Add data loader class

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Commits on Aug 16, 2023

• FIX: Disable report writing in coreg

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• ENH: Output coregistration transforms

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• ENH: Hook up fieldmaps to BOLD processing

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• FIX: Badtab

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Commits on Aug 17, 2023

• ENH: Sink boldref2fmap transforms

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Commits on Aug 21, 2023

• RF: Split fMRIPrep into fit and derivatives workflows (#2913)

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Commits on Aug 22, 2023

• MNT: Add git-annex, datalad, datalad-osf to install environment

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• ENV: Sync scientific python packages to avoid duplication; update Docker install

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Commits on Aug 23, 2023

• Merge branch 'upstream/master' into next

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• FIX: Use unwarp_wf directly on reference

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• FIX: Convert boldref2fmap transforms to ITK text format

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• FIX: Update connections to unwarp_wf, convert ITK transforms to text (#3077)

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• FIX: Match node name to variable name

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• Merge remote-tracking branch 'upstream/master' into next

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• Drop unused functions from workflows.bold.fit

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• RF: Only register boldref2fmap if not found, handle transforms consistently

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• RF: Generate derivative cache per-BOLD, get one-way transforms

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• FIX: Fix name of anatomical workflow

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• FIX: Unused imports, undefined variables

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• FIX: Load IO spec from correct location

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• CFG: Update config for easier debugging

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Commits on Aug 24, 2023

• RF: Generate t1w_brain from t1w and mask on demand for coregistration

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• RF: Update derivative cache spec, calculate per-BOLD, reuse boldref2fmap (#3078)

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• CI: Stop testing legacy output layout

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• CI: Stop testing legacy layout (#3079)

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• CI: Add next to GHA branches

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• ENH: Add --level flag

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Commits on Aug 25, 2023

• ENH: Start reinserting surface stages

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Commits on Aug 28, 2023

• RF: Split estimator finding into helper function

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• ENH: Use refactored surface workflows to generate surfaces and ribbon

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• MNT: Require Python 3.10+

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• ENH: Save surface derivatives

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• MNT: Use nipreps@next again

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Commits on Aug 29, 2023

• ENH: Generate anatomical derivatives useful for resampling (#3081)

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• FIX: Update name for anat_ribbon input

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• CLI: Leave --level free-form for now

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• FIX: Save figures to fmriprep_dir

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• ENH: Add reporting workflow for BOLD fit

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• ENH: Add white matter segmentation to reportlets

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• RF: Select then resample; nipype disallows GenericLabel

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Commits on Aug 30, 2023

• RF: Use SimpleBeforeAfterRPT from nireports

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• ENH: Create fieldmap registration report

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Commits on Aug 31, 2023

• RPT: Apparently Oscar already wrote this caption

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• RPT: Re-add summary and validation reports

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• FIX: Set default SDC to None

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Commits on Sep 1, 2023

• RPT: Small touch-ups to reports

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Commits on Sep 5, 2023

• RPT: Restore subject and execution summary reports

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Commits on Sep 6, 2023

• ENH: Add reporting workflow for BOLD fit (#3082)

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Commits on Sep 27, 2023

• Merge remote-tracking branch 'upstream/master' into next

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Commits on Oct 3, 2023

• FIX: Connect EPI-to-fieldmap transform (#3099)

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Commits on Oct 7, 2023

• Merge remote-tracking branch 'upstream/master' into next

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Commits on Oct 12, 2023

• FIX: Minor fixes to work with MSMSulc-enabled smriprep-next (#3098)

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• FIX: Swap direction of fmap-EPI transform

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• MNT: Bump version requirements (#3107)

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Commits on Oct 15, 2023

• Merge remote-tracking branch 'upstream/master' into next

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Commits on Oct 17, 2023

• RF: Update primary bold workflow to incorporate single shot resampling (#3114)

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• ENH: Check for bold length before building workflow

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• RF: Delete pieces already rewritten

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• ENH: Add generic resampling workflow, use for anatomical

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• ENH: Add interpolation parameters to resampling interface

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• STY: Black

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• RF: Rename functions to match usage

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• ENH: Add general volumetric datasink workflow

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Commits on Oct 18, 2023

• ENH: Hook up anatomical derivatives workflow

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• FIX: Names, connections, metadata

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Commits on Oct 23, 2023

• FIX volumetric

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• FIX: fmapreg_xfm -> boldref2fmap_xfm

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• FIX: Connect target_ref_file in volumetric resample workflow

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• RF: Move coordinate copies into threads to delay allocation

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• FIX: Add sampling reference

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• ENH: Construct resampled data array in F order

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• LOG: Move logging into init_bold_wf

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• RF: Remove old t1 workflow

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• RF: Move resampling to "full" section

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Commits on Oct 26, 2023

• Apply suggestions from code review

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• ENH: Restore resampling to T1w target (#3116)

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Commits on Nov 2, 2023

• ENH: Resample BOLD series to volumetric templates

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• DBG: Better reporting for ANTs h5 parsing failures

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• ENH: Handle warp fields with other sizes

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• RF: Handle no-warp H5 files

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Commits on Nov 3, 2023

• Update fmriprep/utils/transforms.py

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• ENH: Restore resampling BOLD to volumetric templates (#3121)

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• RF: Reverse direction of bold-T1w transform

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• ENH: Restore confound regressor generation as part of full

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• RF: Move confounds datasink into bold_wf

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Commits on Nov 7, 2023

• ENH: Restore confound generation (#3120)

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• RF: Remove datasinks already reimplemented elsewhere

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• ENH: Restore resampling to FreeSurfer surfaces

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• FIX: Moving and reference apply to the forward transform, not the final

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Commits on Nov 13, 2023

• ENH: Restore resampling to surface GIFTIs (#3126)

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• ENH: Pull anatomical inputs to CIFTI through

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• ENH: Restore CIFTI-2 generation

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• FIX: Set ROI data before writing array, use uint8

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• FIX: Only connect template_iterator_wf if it exists

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• DOC: Complete docstring first line

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• FIX: Do not sink BOLD on the main thread

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• ENH: Restore CIFTI-2 generation (#3129)

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Commits on Nov 14, 2023

• MNT: Shift more config into env.yml

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• MNT: Bump environment

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• MNT: Bump environment (#3132)

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• ENH: Restore carpetplot workflow

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• RPT: Update boilerplate on new bold_wf

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• DOC: Update init_bold_wf docstring

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• RF: Remove dead code

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• STY: Pacify flake8 a bit

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• DOC: Update installation guide

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• DOC: Update usage.rst with notes on reusing derivatives

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• DOC: Update workflow graph generators

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• FIX: Incomplete transition to an HMC-free path

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• DOC: Add notes on processing level to outputs.rst

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• ENH: Restore carpetplot and other final adjustments (#3131)

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Commits on Nov 15, 2023

• MNT: Update NodeJS, svgo and bids-validator

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• FIX: Pass bold file to ds_fmapreg_wf to get correct naming

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• CI: Remove legacy outputs, update ds005 fasttrack outputs

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Commits on Nov 16, 2023

• FIX: Add ds054 and ds210 fastrack outputs [no fasttrack]

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• CFG: Remove hacks intended to ease development

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• RF: Remove old copy of _create_mem_gb

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• DOC: Add docstring for init_bold_volumetric_resample_wf

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• CI: Update full output listings

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• RF: Remove reporting from coregistration workflows

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• RF: Remove unused bold_t1_trans_wf

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• RF: Drop VolumeToSurfaceMapping output weights

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• CI: Restore expected outputs checks

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• FIX: Use msmsulc registration

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• RF: Listify and sort BOLD series by EchoTime once [no fasttrack]

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Commits on Nov 18, 2023

• ENH: Restore STC reporting to summary

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• FIX: Pass fmriprep output directory to anatomical workflow

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• FIX: Correctly generate resampling reference, pass to downstream resamplers

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Commits on Nov 19, 2023

• Final revisions for next branch (#3134)

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• ENH: Add volumetric and CIFTI anatomical outputs

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• RF: Reuse cortical mask ROI and downsampled midthickness

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• FIX: Ensure BOLD is not oversampled for anat

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• DOCKER: Bump npm install line

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• CI: Update expected outputs [no fasttrack]

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• RF: Write out anatomical template derivatives (#3136)

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• DOC: Add initial release notes for 23.2.0

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Commits on Nov 20, 2023

• MNT: smriprep-next has been merged

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• DOC: Update expected outputs, note minimal derivatives

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• RPT: Improve and align captions with now-produced reportlets [no fasttrack]

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• chore: update to latest migas api

  

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• chore: update to latest migas api (#3138)

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• Update Dockerfile

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• Update Dockerfile

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Commits on Nov 21, 2023

• DOC: Improve report captions and update expected outputs in docs (#3137)

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• FIX: Custom error handling

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• DOC: Expand release notes

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