Code

RF: Move to fit/apply workflow#360

Code

Merged

mgxd merged 142 commits intonipreps:masternipreps/nibabies:masterfrom mgxd:rf/fit-applymgxd/nibabies:rf/fit-applyCopy head branch name to clipboardAug 1, 2024

+13,485-9,911

Commits

Commits on Mar 28, 2024

• MAINT: Update dependencies, move to ruff

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  97aef93

• MAINT: Update dependencies

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  89c3198

• CHORE: Add Thomas to contributors

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  0024278

• RF[WIP]: Start fit-apply

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  d7f8866

Commits on Apr 2, 2024

• RF: Clean up segmentation workflow

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  4c50c8d

Commits on Apr 3, 2024

• STY: Single connect formatting, add log message

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  44f02dd

• ENH[WIP]: More fitting

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  fbdd679

• ENH: Add segmentation fit step

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  1a147de

Commits on Apr 4, 2024

• ENH[WIP]: Add template normalization, imports, type annots

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  7ea329a

Commits on Apr 10, 2024

• ENH: Add surface recon logic, move towards single anatomical reference

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  c1e19ed

• ENH: Add mask refinement, rework T1w mask logic

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  a0dbf7c

Commits on Apr 11, 2024

• ENH: Handle surfaces/morphometrics/fsLR registration

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  9138398

Commits on Apr 12, 2024

• ENH: Simplify mcribs/infantfs workflows

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  96b3f8a

Commits on Apr 15, 2024

• ENH: Add symbolic copy of sphere.reg to make FS integration easier

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  f14e816

• FIX: Simplify dhcp reg workflow, remove crud

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  0e2c2a2

• FIX: Insert new parameters, update mcribs -> fslr workflow

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  b93349e

• RF: Contrast -> image type

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  9452907

• RF: Move fit to anatomical workflows module

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  f3e4204

Commits on Apr 18, 2024

• FIX: T2w brainmask, move precomputed to dict

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  bd851ce

• ENH: Add top-level anat workflow

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  502cca2

• RF: Drop derivatives class for dict approach

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  57f6053

• ADD: Expected anatomical files

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  b6ca0ab

Commits on Apr 19, 2024

• RF: Make midthickness creation standalone workflow

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  cdbfbd2

• FIX: Anat IO, brain extraction inputs

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  c8b8f24

• RF: Brain extraction parameters, typing

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  1eaf43e

Commits on Apr 23, 2024

• RF: Branch fsLR resampling if using mcribs recon

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  3168621

• ADD: Midthickness resampling workflow for MCRIBS

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  9b455af

• RF: Determine reference anatomical prior to fit workflow

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  5ac10ed

Commits on Apr 24, 2024

• ENH: Add fingerprint file to quickly determine MCRIB runs

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  8f56476

• ENH: Beef up anatomical summary

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  161e66a

Commits on Apr 25, 2024

• ENH: Add new parser options

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  034620b

• ENH: Reflect new options within configuration

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  5cb53e0

• FIX: Add session label when fetching derivatives

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  d67ad10

• FIX: Proper typing, parameters

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  224f6a1

• ENH: Add anatomical processing

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  cbc4cb3

• PIN: smriprep working branch

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• CHORE: Update build requirements

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  fb7255c

• DOCKER: Update micromamba step

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  6fc8509

• FIX: Traits version

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  23a0d24

Commits on Apr 26, 2024

• FIX: Determine which surface recon method to use, by default

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  a94f627

• PIN: niworkflows branch

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  f2e685e

• FIX: Remove eager imports

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  8e0becf

• FIX: Connections, missed parameters

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  d5066aa

• FIX: Use template iterator in anat reports

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  665309a

• ENH: output both forward and reverse coreg transforms

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• FIX: fstring + quotes

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• ENH: Add named derivatives support

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  0fc5d04

• FIX: Fetch other anatomical files

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• more workflow fixes

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• DOCKER: Debug build

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  c74ca50

Commits on Apr 28, 2024

• DKR: Add step to install traits, /src/nibabies->/src

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  f717888

• MAINT: Update new --patch path

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  dcfcfcd

• FIX: Connections

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Commits on Apr 29, 2024

• ENH: Add pdb debug mode

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  cbc1826

• FIX: Misfired connections

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  567e007

• FIX: aaand more missing/incorrect connections

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  cb13b5b

• RF: Add "apply" workflow to facilitate fit caching

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  32d9be5

Commits on May 1, 2024

• FIX: Remove mcribs templates hack now that they are on templateflow

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  5e1f064

• FIX: Ensure midthickness is saved to subjects_dir

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  58a9c10

• ENH: Clean up dual anat workflow, port logic to single anat

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  c5d6365

• ENH: Finalize single anat workflow

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  2d94ad1

Commits on May 2, 2024

• RF: Specify T1w/T2w space in derivatives

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  1a0be93

• FIX: Specify space on outputs that may be in T1w/T2w space

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  2ec91e7

• DKR: Cache new templates

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  bdcd452

• FIX: Handle case of multiple T1w files

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  67feb16

• FIX: Catch errors with basic, no derivatives, processing

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  4e2b238

• FIX: Add entrypoint for single anat workflow, prioritize recon_method for anat ref

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  8d40176

• FIX: Remove superfluous denoise

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  c10d842

Commits on May 6, 2024

• FIX: Single anat problems (T2-only)

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Commits on May 7, 2024

• FIX: Port bold2anat feature into BOLD workflow

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Commits on May 10, 2024

• FIX: Handle some derivatives but not preproc

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  0c2fce3

Commits on May 15, 2024

• WIP: BOLD registration fit/apply

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  69fa824

• DOCS: Start outlining outputs

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• DOCS: Flesh out outputs from fmriprep

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  e8153c7

• FIX: Actually fetch templates

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  aedfca9

• WIP: Port over bold processing helpers

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• WIP: Functional integration

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• WIP/STY: Ruff bold workflows

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• WIP: functional - anatomical coregistration

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Commits on May 16, 2024

• WIP: Modernize resampling

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• WIP: Update BOLD to use reference anatomical

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  65ffaac

• RF: Consider changing FAST inputs based on T1w/T2w image

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• ENH: Add BIDSURI interface (should move to niworkflows)

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• WIP: Port updated confounds workflow

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  3bb6727

• FIX: T1w->anat inputs

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• WIP: Add apply workflow

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• WIP: Add resampling tools

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• WIP: HMC workflow

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• WIP: Update confound interfaces

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• ENH: Add functional derivatives crawler

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• FIX: Functional workflow connections

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• ENH: Alternative boldref workflow

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• FIX: Imports, default dismiss entities

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  ee35efe

• FIX: fmriprep->nibabies

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• ENH: Modernize config

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• FIX: Update FunctionalSummary with new bold2anat_init options

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• ENH: Add Sources

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• RF: more fmriprep->nibabies

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Commits on May 17, 2024

• FIX: Minimal

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  073b705

• ENH: Drop early BOLD frames from boldref calculation

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  aa7670f

Commits on May 24, 2024

• FIX: Avoid carpetplot unless CIFTI outputs

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• RF: Move anatomical apply into separate module

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  821a0a7

• FIX: Update base workflows to reflect previous changes

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Commits on May 30, 2024

• FIX: Reverse size params, remove pesky warning

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  d9c6c1c

• DKR: Cache MNI templates to avoid cache invalidation

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  2e7e583

• ENH: Re-add subcortical ROI alignment for dtseries output

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Commits on Jun 3, 2024

• RF: Split segmentation datasink into single, reusable wf

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• FIX: Segmentation indexes

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• RF: Func io spec

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• DOC: Fix reporting

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• RF: Do not connect from ds_ node to avoid cache invalidation

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Commits on Jun 4, 2024

• FIX: Move select node out of loop

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• RF: Reorganize warp transpose

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• RM: Template files now available in templateflow

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• CI/STY: Fix spelling errors, update style check

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Commits on Jun 7, 2024

• FIX: Slicetiming

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Commits on Jun 10, 2024

• FIX: Ensure libitk matches ANTs expectation

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• chore: bump niworkflows to master

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Commits on Jul 10, 2024

• FIX: Pass anat2std xfm to BOLD workflow

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Commits on Jul 11, 2024

• ADD: Option to ensure output directory is fully populated

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• ENH: Bump patched MCRIBS

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  15327e1

• FIX: Update FS->MCRIBS label mappings

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Commits on Jul 15, 2024

• FIX: Do not use FAST if precomputed aseg is available

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  d7abbef

Commits on Jul 18, 2024

• FIX: Single anat template name

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• FIX: Template anatomical reporting

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  5ad69eb

• FIX: Boilerplate file as string

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Commits on Jul 22, 2024

• ENH/FIX: Make BOLD HMC start frame configurable, do not clip BOLD timeseries

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Commits on Jul 24, 2024

• FIX: Stringify output directory

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Commits on Jul 29, 2024

• MAINT: Bump preps to pre-release master branches

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• FIX: Remove libitk hack

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Commits on Jul 30, 2024

• MAINT: Update dependency pins

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• CHORE: Remove crud

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• Remove ICA AROMA

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Commits on Jul 31, 2024

• TST: Update config test

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  6bd037c

• FIX: Clean up pyproject

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• FIX: Data intake

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• TST: Add acres, test derivatives intake

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• TST: Create new derivatives test

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• MAINT: Exclude non-source files from checks

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• STY: Mass ruff-ication

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Commits on Aug 1, 2024

• chore: pin preps to latest releases

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• FIX: Revert wrapper to PY2 compatibility

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