Code

sMRIPrep 0.13#376

Code

Merged

effigies merged 143 commits intomasternipreps/smriprep:masterfrom nextnipreps/smriprep:nextCopy head branch name to clipboardNov 20, 2023

+3,437-1,801

Commits

Commits on Nov 30, 2022

• RF: Split surface workflow into recon and derivative preparation

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• MNT: Update .gitignore

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  9dfa265

• RF: Break derivatives worfklow into first and second derivatives

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  9b9a5ce

• RF: Split workflows.norm into workflows.fit.registration and workflows.apply.resampling

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• RF: Use split workflows in anat_preproc_wf

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• RF: Factor out brainmask refinement workflow

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  5f152d9

• RF: Reorganize anat into fit and derivatives

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• FIX: Continue on missing fast-track items

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  37aade1

• RF: Deprecate --fast-track for --derivatives

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• ENH: Add logging during workflow build

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• WRAPPER: Patch in derivatives

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• RF: Use pre-computed template warps

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• RF: Split first derivatives workflow

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  5b07196

• ENH: Use ITK transforms in FreeSurfer contexts

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• FIX: Workflow connections

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  d47338b

• RF: Drop unused predict_derivatives function

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• RF: Skip fsnative registration if transform is found

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• STY: Unused import

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• DOC: Add precomputed arg to workflow, remove old output

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  ee28819

• FIX: Add fit_wf.inputnode explicitly

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• MNT: Re-add workflow description

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• Add types to workflow parameters

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• DOC: Restore docstring for anat_fit_wf, update argument ordering

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  e12ee79

• DOC: Update output docs, make a note of organization

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  52c7994

• FIX: Drop t1w_realign_xfm from outputnodes

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  257a5c8

• DOC: Update anat_preproc_wf arguments and docs

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• STY: black

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  a31959d

• FIX: Un-split badly split f-string

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• RF: Re-attach report workflow

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  b4ae477

• DOC: Fix docstring

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• DOC: Templateflow cannot be mocked if we import niworkflows.utils.spaces

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  95f7336

• FIX: Guard against missing references

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• Drop apply workflows for now

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Commits on Apr 11, 2023

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

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• ENH: Clean up t2w_preproc sinking

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Commits on Apr 16, 2023

• CI: Drop unused fs-license context

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  b401197

• FIX: Re-add anat_preproc_wf outputs

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• FIX: Clearer skull strip variables

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• ENH: Move anat ribbon out of primary fit workflow

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  066b531

• FIX: Disable validation on derivative dataset

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  bfd418b

• FIX: Connect ANTs segmentation from n4-only wf

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

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• DOC: Add t2w arg in docstring

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Commits on Jun 6, 2023

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

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• RF: Move sphere_reg_wf into surface derivatives

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Commits on Jun 19, 2023

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

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• STY: black; adapt flake8 rules

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

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Commits on Aug 25, 2023

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

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Commits on Aug 27, 2023

• RF: Break morphometry and surface resampling into separate workflows

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• FIX: Wait on save_midthickness to complete recon

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• RF: Make transform optional for normalizing GIFTIs

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• RF: Only purge VolGeom metadata for surfaces we convert --to-scanner

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• RF: Split sphere_reg conversion from fsLR registration

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• ENH: Add --cifti-output flag and test

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• RF: Remove unused connection, pass density value directly

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• FIX: Retrieve "graymid", not "midthickness"

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• CI: Use fresh workdir cache

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• FIX: Drop sphere_reg from default surfaces

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• RF: Rewrite surface fetcher to prefer midthickness

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• FIX: Pass surfaces after node creation

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  42abe8d

• FIX: Get this thing to work

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• DEBUG: Set some debug config

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• RF: Pass white/pial directly to anat_ribbon_wf

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• CI: Expect morphometry CIFTI files

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Commits on Aug 28, 2023

• RF: Split out surface derivative workflow

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  8092b24

• Update smriprep/interfaces/surf.py

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• Merge pull request #360 from effigies/rf/split_surface_workflows

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  8bdd2ce

• CI: Drop Python 3.8 (for now)

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• CI: Run Github actions on PRs to next

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• MNT: 3.10+

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• ENH: Run pytest on CircleCI

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• Merge pull request #364 from effigies/ci/pytest-on-circle

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• ENH: Add simple Python interface to generate ribbon

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• TEST: Add test for MakeRibbon interface

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• TEST: Integration test with gifti_surfaces and anat_ribbon workflows

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• CI: Attach to the get_data workspace to have the FS_LICENSE

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  5bd3b74

• FIX: Inverted logic

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• RF: Replace fslmaths chain with MakeRibbon

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• TEST: Fix double call and skip check for fslmaths

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Commits on Aug 29, 2023

• Update smriprep/interfaces/surf.py

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• Update smriprep/interfaces/surf.py

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• DOC: Add docstring for anat_ribbon_wf

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• Merge pull request #363 from effigies/enh/simplify-ribbon

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Commits on Aug 31, 2023

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

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Commits on Sep 6, 2023

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

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• FIX: msm_sulc does not currently reside in fit

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• FIX: Update msm_sulc connections

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

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Commits on Sep 7, 2023

• ENH: Save msm registration sphere as desc-msm_sphere.surf.gii (#365)

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Commits on Sep 28, 2023

• ENH: Update iospec to retrieve surfaces

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• ENH: Tag log entries with ANAT to separate from other workflows

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• ENH: Add msmsulc to fit workflow

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Commits on Sep 29, 2023

• ENH: Add surface outputs to fit outputnode

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• RF: Remove fit derivatives from secondary workflow

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  fcd3b70

• FIX: Update outputnode spec, restore anat_ribbon

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  fe7332b

• RF: Move anat_ribbon into fit workflow for efficiency

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  53cb30c

• FIX: Drop unused std_xfms and get_outputnode_spec()

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  71aa027

• DOC: Fix workflow graph creation

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  7dba95b

• FIX: Various connections and names

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• CI: Authenticate Docker image pulls

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• FIX: Update collect_derivatives call

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• FIX: Remove defunct collect_derivatives code

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• CI: Expect ribbon_mask.json

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Commits on Oct 2, 2023

• RF: Switch to more targeted morphometry datasinks

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Commits on Oct 11, 2023

• Merge pull request #370 from effigies/enh/fit-msmsulc

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

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Commits on Oct 14, 2023

• Apply suggestions from code review

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Commits on Nov 8, 2023

• FIX: Cleanup bad commit/merge/something

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Commits on Nov 9, 2023

• FIX: Update surfaces with fsnative2t1w_xfm

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• Merge pull request #384 from effigies/fix/transform_surfs

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• ENH: Add interface to invert shape files

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• FIX: Invert sulcal depth metric before passing to MSM

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• DATA: Add atlases from DCAN-HCP

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• FIX: Use DCAN-HCP atlases for MSMSulc

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• MNT: Treat GIFTIs as binary for merging and running git-diff

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• Merge pull request #383 from effigies/fix/msm-invert-sulc

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Commits on Nov 10, 2023

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

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

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Commits on Nov 13, 2023

• FIX: Missing JSON brace

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• MNT: Refine pre-commit exclusions

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• STY: Apply pre-commit

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Commits on Nov 15, 2023

• ENH: Annotate mris_expand with thread usage

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Commits on Nov 16, 2023

• Update smriprep/interfaces/freesurfer.py

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Commits on Nov 17, 2023

• MNT: Remove AFNI from smriprep docker container

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Commits on Nov 18, 2023

• Merge pull request #387 from effigies/docker/drop-afni

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• Merge pull request #386 from effigies/enh/multithread-mrisexpand

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Commits on Nov 19, 2023

• RF: Generalize InvertShape to MetricMath

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• RF: Move InvertSulc to MetricMath, update imports

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• ENH: Add workflow to convert HCP-style morphometry GIFTIs

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• ENH: Add workflow to resample GIFTIs to fsLR and generate CIFTIs

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• RF: Add template-space datasink workflow, iterate in main workflow

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• RF: Add CIFTI morphometrics datasink workflow

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• FIX: std2anat -> anat2std_xfm in ds_std_volumes_wf connection

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• FIX: Only create CIFTI workflows if cifti_output is set

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• DOC: Checkpoint SpatialReferences in docstring workflows

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• DOC: Add omp_nthreads to init_morph_grayords_wf() docstring

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• FIX: hcp_morphometrics_wf connection

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• RF: Separate midthickness resampling from morphometry resampling

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• ENH: Reconnect datasinks

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• FIX: Fetch MSM registration from correct buffer

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• Merge pull request #388 from effigies/rf/template-resampling-workflows

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• Apply suggestions from code review

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