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sMRIPrep 0.13 #376

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Nov 20, 2023
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8e8eea9
RF: Split surface workflow into recon and derivative preparation
effigies Sep 30, 2022
9dfa265
MNT: Update .gitignore
effigies Sep 30, 2022
9b9a5ce
RF: Break derivatives worfklow into first and second derivatives
effigies Oct 3, 2022
fe60be3
RF: Split workflows.norm into workflows.fit.registration and workflow…
effigies Oct 11, 2022
de8e62b
RF: Use split workflows in anat_preproc_wf
effigies Oct 11, 2022
5f152d9
RF: Factor out brainmask refinement workflow
effigies Oct 18, 2022
58b8a3a
RF: Reorganize anat into fit and derivatives
effigies Nov 1, 2022
37aade1
FIX: Continue on missing fast-track items
effigies Nov 9, 2022
54bbc2e
RF: Deprecate --fast-track for --derivatives
effigies Nov 9, 2022
27a4d97
ENH: Add logging during workflow build
effigies Nov 9, 2022
5d2b755
WRAPPER: Patch in derivatives
effigies Nov 9, 2022
73eb03f
RF: Use pre-computed template warps
effigies Nov 10, 2022
5b07196
RF: Split first derivatives workflow
effigies Nov 14, 2022
890fc3e
ENH: Use ITK transforms in FreeSurfer contexts
effigies Nov 14, 2022
d47338b
FIX: Workflow connections
effigies Nov 14, 2022
7429106
RF: Drop unused predict_derivatives function
effigies Nov 14, 2022
c1f022e
RF: Skip fsnative registration if transform is found
effigies Nov 14, 2022
3123fbd
STY: Unused import
effigies Nov 14, 2022
ee28819
DOC: Add precomputed arg to workflow, remove old output
effigies Nov 15, 2022
dca427e
FIX: Add fit_wf.inputnode explicitly
effigies Nov 15, 2022
dc5eb34
MNT: Re-add workflow description
effigies Nov 16, 2022
4f6369c
Add types to workflow parameters
effigies Nov 16, 2022
e12ee79
DOC: Restore docstring for anat_fit_wf, update argument ordering
effigies Nov 16, 2022
52c7994
DOC: Update output docs, make a note of organization
effigies Nov 16, 2022
257a5c8
FIX: Drop t1w_realign_xfm from outputnodes
effigies Nov 16, 2022
ada61ac
DOC: Update anat_preproc_wf arguments and docs
effigies Nov 16, 2022
a31959d
STY: black
effigies Nov 16, 2022
cf96ab5
FIX: Un-split badly split f-string
effigies Nov 16, 2022
b4ae477
RF: Re-attach report workflow
effigies Nov 18, 2022
b1f4c5c
DOC: Fix docstring
effigies Nov 19, 2022
95f7336
DOC: Templateflow cannot be mocked if we import niworkflows.utils.spaces
effigies Nov 29, 2022
c7d9101
FIX: Guard against missing references
effigies Nov 29, 2022
8aa8e6c
Drop apply workflows for now
effigies Nov 30, 2022
653f728
Merge remote-tracking branch 'upstream/master' into rf/split_workflow
effigies Apr 11, 2023
73be00f
ENH: Clean up t2w_preproc sinking
effigies Apr 11, 2023
b401197
CI: Drop unused fs-license context
effigies Jan 18, 2023
05f9cc9
FIX: Re-add anat_preproc_wf outputs
effigies Jan 19, 2023
a5f64fc
FIX: Clearer skull strip variables
effigies Jan 19, 2023
066b531
ENH: Move anat ribbon out of primary fit workflow
effigies Apr 14, 2023
bfd418b
FIX: Disable validation on derivative dataset
effigies Apr 15, 2023
811f52f
FIX: Connect ANTs segmentation from n4-only wf
effigies Apr 16, 2023
1dcac89
Merge remote-tracking branch 'upstream/master' into rf/split_workflow
effigies Apr 16, 2023
7f66113
DOC: Add t2w arg in docstring
effigies Apr 16, 2023
b07a423
Merge remote-tracking branch 'upstream/master' into rf/split_workflow
effigies Jun 6, 2023
39f5dea
RF: Move sphere_reg_wf into surface derivatives
effigies Jun 6, 2023
a7a42e5
Merge remote-tracking branch 'upstream/master' into rf/split_workflow
effigies Jun 19, 2023
b771ae0
STY: black; adapt flake8 rules
effigies Jun 19, 2023
c8853ef
Merge remote-tracking branch 'upstream/master' into rf/split_workflow
effigies Jun 19, 2023
311328c
Merge remote-tracking branch 'upstream/master' into next
effigies Aug 25, 2023
ab82e3f
RF: Break morphometry and surface resampling into separate workflows
effigies Aug 25, 2023
4393012
FIX: Wait on save_midthickness to complete recon
effigies Aug 27, 2023
2725048
RF: Make transform optional for normalizing GIFTIs
effigies Aug 27, 2023
3e4f185
RF: Only purge VolGeom metadata for surfaces we convert --to-scanner
effigies Aug 27, 2023
9d0d4a0
RF: Split sphere_reg conversion from fsLR registration
effigies Aug 27, 2023
0ac6ec9
ENH: Add --cifti-output flag and test
effigies Aug 27, 2023
48b57cf
RF: Remove unused connection, pass density value directly
effigies Aug 27, 2023
86821b6
FIX: Retrieve "graymid", not "midthickness"
effigies Aug 27, 2023
ee9fff7
CI: Use fresh workdir cache
effigies Aug 27, 2023
bd097e8
FIX: Drop sphere_reg from default surfaces
effigies Aug 27, 2023
776a90d
RF: Rewrite surface fetcher to prefer midthickness
effigies Aug 27, 2023
42abe8d
FIX: Pass surfaces after node creation
effigies Aug 27, 2023
fb17bbe
FIX: Get this thing to work
effigies Aug 27, 2023
a54c551
DEBUG: Set some debug config
effigies Aug 27, 2023
f87d17f
RF: Pass white/pial directly to anat_ribbon_wf
effigies Aug 27, 2023
0a9a096
CI: Expect morphometry CIFTI files
effigies Aug 27, 2023
8092b24
RF: Split out surface derivative workflow
effigies Aug 27, 2023
9425caa
Update smriprep/interfaces/surf.py
effigies Aug 28, 2023
8bdd2ce
Merge pull request #360 from effigies/rf/split_surface_workflows
effigies Aug 28, 2023
d1e2090
CI: Drop Python 3.8 (for now)
effigies Aug 28, 2023
0958d89
CI: Run Github actions on PRs to next
effigies Aug 28, 2023
506df71
MNT: 3.10+
effigies Aug 28, 2023
601231e
ENH: Run pytest on CircleCI
effigies Aug 28, 2023
244f1b2
Merge pull request #364 from effigies/ci/pytest-on-circle
effigies Aug 28, 2023
e9c17e5
ENH: Add simple Python interface to generate ribbon
effigies Aug 28, 2023
85550e6
TEST: Add test for MakeRibbon interface
effigies Aug 28, 2023
751369b
TEST: Integration test with gifti_surfaces and anat_ribbon workflows
effigies Aug 28, 2023
5bd3b74
CI: Attach to the get_data workspace to have the FS_LICENSE
effigies Aug 28, 2023
df4d369
FIX: Inverted logic
effigies Aug 28, 2023
e6c972e
RF: Replace fslmaths chain with MakeRibbon
effigies Aug 28, 2023
4624038
TEST: Fix double call and skip check for fslmaths
effigies Aug 28, 2023
e9165a3
Update smriprep/interfaces/surf.py
effigies Aug 29, 2023
fb05822
Update smriprep/interfaces/surf.py
effigies Aug 29, 2023
c3f51ad
DOC: Add docstring for anat_ribbon_wf
effigies Aug 29, 2023
9a135f4
Merge pull request #363 from effigies/enh/simplify-ribbon
effigies Aug 29, 2023
92f2113
Merge remote-tracking branch 'upstream/master' into next
effigies Aug 31, 2023
fe8f7ca
Merge remote-tracking branch 'upstream/master' into next
effigies Sep 6, 2023
c807c7f
FIX: msm_sulc does not currently reside in fit
effigies Sep 6, 2023
8a6fc42
FIX: Update msm_sulc connections
effigies Sep 6, 2023
b065045
Merge remote-tracking branch 'upstream/master' into next
effigies Sep 6, 2023
f6b842f
ENH: Save msm registration sphere as desc-msm_sphere.surf.gii (#365)
effigies Sep 7, 2023
e59f912
ENH: Update iospec to retrieve surfaces
effigies Sep 28, 2023
70a94da
ENH: Tag log entries with ANAT to separate from other workflows
effigies Sep 28, 2023
3a0f20d
ENH: Add msmsulc to fit workflow
effigies Sep 28, 2023
4e69c3b
ENH: Add surface outputs to fit outputnode
effigies Sep 29, 2023
fcd3b70
RF: Remove fit derivatives from secondary workflow
effigies Sep 29, 2023
fe7332b
FIX: Update outputnode spec, restore anat_ribbon
effigies Sep 29, 2023
53cb30c
RF: Move anat_ribbon into fit workflow for efficiency
effigies Sep 29, 2023
71aa027
FIX: Drop unused std_xfms and get_outputnode_spec()
effigies Sep 29, 2023
7dba95b
DOC: Fix workflow graph creation
effigies Sep 29, 2023
948b989
FIX: Various connections and names
effigies Sep 29, 2023
33a7593
CI: Authenticate Docker image pulls
effigies Sep 29, 2023
6730539
FIX: Update collect_derivatives call
effigies Sep 29, 2023
e3b87eb
FIX: Remove defunct collect_derivatives code
effigies Sep 29, 2023
b49ac4c
CI: Expect ribbon_mask.json
effigies Sep 29, 2023
3b5b230
RF: Switch to more targeted morphometry datasinks
effigies Oct 2, 2023
92773f5
Merge pull request #370 from effigies/enh/fit-msmsulc
effigies Oct 11, 2023
6995f33
Merge remote-tracking branch 'upstream/master' into next
effigies Oct 11, 2023
116cad9
Apply suggestions from code review
effigies Oct 14, 2023
05ae8c5
FIX: Cleanup bad commit/merge/something
effigies Nov 8, 2023
477063c
FIX: Update surfaces with fsnative2t1w_xfm
effigies Nov 9, 2023
e370a73
Merge pull request #384 from effigies/fix/transform_surfs
effigies Nov 9, 2023
cc744fb
ENH: Add interface to invert shape files
effigies Nov 8, 2023
357cb5f
FIX: Invert sulcal depth metric before passing to MSM
effigies Nov 8, 2023
ca55630
DATA: Add atlases from DCAN-HCP
effigies Nov 9, 2023
c6246bc
FIX: Use DCAN-HCP atlases for MSMSulc
effigies Nov 9, 2023
b52fd5c
MNT: Treat GIFTIs as binary for merging and running git-diff
effigies Nov 9, 2023
c238409
Merge pull request #383 from effigies/fix/msm-invert-sulc
effigies Nov 9, 2023
619b157
Merge remote-tracking branch 'upstream/master' into next
effigies Nov 10, 2023
55605ec
Merge remote-tracking branch 'upstream/master' into next
effigies Nov 10, 2023
cfc0592
FIX: Missing JSON brace
effigies Nov 13, 2023
c7e9c1d
MNT: Refine pre-commit exclusions
effigies Nov 13, 2023
b5e8663
STY: Apply pre-commit
effigies Nov 13, 2023
43eed0e
ENH: Annotate mris_expand with thread usage
effigies Nov 15, 2023
899f2f4
Update smriprep/interfaces/freesurfer.py
effigies Nov 16, 2023
de41f41
MNT: Remove AFNI from smriprep docker container
effigies Nov 17, 2023
1c00cee
Merge pull request #387 from effigies/docker/drop-afni
effigies Nov 18, 2023
6ce2121
Merge pull request #386 from effigies/enh/multithread-mrisexpand
effigies Nov 18, 2023
dfc26ff
RF: Generalize InvertShape to MetricMath
effigies Nov 19, 2023
76edb42
RF: Move InvertSulc to MetricMath, update imports
effigies Nov 19, 2023
58276c0
ENH: Add workflow to convert HCP-style morphometry GIFTIs
effigies Nov 19, 2023
d9f1bff
ENH: Add workflow to resample GIFTIs to fsLR and generate CIFTIs
effigies Nov 19, 2023
22fd48d
RF: Add template-space datasink workflow, iterate in main workflow
effigies Nov 19, 2023
36029c0
RF: Add CIFTI morphometrics datasink workflow
effigies Nov 19, 2023
808889b
FIX: std2anat -> anat2std_xfm in ds_std_volumes_wf connection
effigies Nov 19, 2023
7c5802f
FIX: Only create CIFTI workflows if cifti_output is set
effigies Nov 19, 2023
373c8ed
DOC: Checkpoint SpatialReferences in docstring workflows
effigies Nov 19, 2023
25a9769
DOC: Add omp_nthreads to init_morph_grayords_wf() docstring
effigies Nov 19, 2023
5edd05f
FIX: hcp_morphometrics_wf connection
effigies Nov 19, 2023
a08d9cf
RF: Separate midthickness resampling from morphometry resampling
effigies Nov 19, 2023
afa5620
ENH: Reconnect datasinks
effigies Nov 19, 2023
0bf46d1
FIX: Fetch MSM registration from correct buffer
effigies Nov 19, 2023
3c2edb7
Merge pull request #388 from effigies/rf/template-resampling-workflows
effigies Nov 19, 2023
d7bda97
Apply suggestions from code review
effigies Nov 19, 2023
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46 changes: 36 additions & 10 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ _machine_defaults: &machine_defaults
_python_defaults: &python_defaults
docker:
- image: cimg/python:3.10.9
auth:
username: $DOCKER_USER
password: $DOCKER_PAT
working_directory: /tmp/src/smriprep

_docker_auth: &docker_auth
Expand Down Expand Up @@ -43,6 +46,9 @@ _pull_from_registry: &pull_from_registry
docs_deploy: &docs
docker:
- image: node:8.10.0
auth:
username: $DOCKER_USER
password: $DOCKER_PAT
working_directory: /tmp/gh-pages
steps:
- run:
Expand Down Expand Up @@ -282,8 +288,10 @@ jobs:
paths:
- /home/circleci/.local

test_wrapper:
test:
<<: *machine_defaults
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
steps:
- attach_workspace:
at: /tmp
Expand Down Expand Up @@ -323,6 +331,24 @@ jobs:
which smriprep-docker
smriprep-docker -i nipreps/smriprep:latest --help
smriprep-docker -i nipreps/smriprep:latest --version
- restore_cache:
keys:
- testdata-v2-{{ .Branch }}-{{ epoch }}
- testdata-v2-{{ .Branch }}
- testdata-v2-
- restore_cache:
keys:
- templateflow-v1-{{ .Branch }}-{{ epoch }}
- templateflow-v1-{{ .Branch }}
- templateflow-v1-
- run:
name: Run Pytest
no_output_timeout: 2h
command: |
bash /tmp/src/smriprep/.circleci/pytest.sh
- codecov/upload:
file: /tmp/data/pytest_cov.xml
flags: pytest

test_deploy_pypi:
<<: *python_defaults
Expand Down Expand Up @@ -414,9 +440,10 @@ jobs:
- run: *pull_from_registry
- restore_cache:
keys:
- ds005-anat-v9-{{ .Branch }}-{{ epoch }}
- ds005-anat-v9-{{ .Branch }}
- ds005-anat-v9-master
- ds005-anat-v0-{{ .Branch }}-{{ epoch }}
- ds005-anat-v0-{{ .Branch }}
- ds005-anat-v0-master
- ds005-anat-v0-next
effigies marked this conversation as resolved.
Show resolved Hide resolved
- restore_cache:
keys:
- testdata-v2-{{ .Branch }}-{{ epoch }}
Expand Down Expand Up @@ -470,7 +497,7 @@ jobs:
rm -rf /tmp/ds005/work/reportlets
rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/
- save_cache:
key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
key: ds005-anat-v0-{{ .Branch }}-{{ epoch }}
paths:
- /tmp/ds005/work

Expand Down Expand Up @@ -772,8 +799,6 @@ workflows:
only: /.*/

- get_data:
context:
- fs-license
filters:
branches:
ignore:
Expand All @@ -793,10 +818,11 @@ workflows:
tags:
only: /.*/

- test_wrapper:
- test:
context:
- nipreps-common
requires:
- get_data
- build
filters:
branches:
Expand Down Expand Up @@ -852,7 +878,7 @@ workflows:
- build_docs
- ds005
- ds054
- test_wrapper
- test
filters:
branches:
only: /master/
Expand All @@ -865,7 +891,7 @@ workflows:
- ds005
- ds054
- test_deploy_pypi
- test_wrapper
- test
filters:
branches:
ignore: /.*/
Expand Down
11 changes: 11 additions & 0 deletions .circleci/ds005_outputs.txt
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ smriprep/sub-01/anat/sub-01_desc-brain_mask.json
smriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
smriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
smriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
smriprep/sub-01/anat/sub-01_desc-ribbon_mask.json
smriprep/sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
smriprep/sub-01/anat/sub-01_dseg.nii.gz
smriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
Expand All @@ -25,7 +26,9 @@ smriprep/sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_sulc.shape.gii
smriprep/sub-01/anat/sub-01_hemi-L_thickness.shape.gii
smriprep/sub-01/anat/sub-01_hemi-L_white.surf.gii
Expand All @@ -34,12 +37,20 @@ smriprep/sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_inflated.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_sulc.shape.gii
smriprep/sub-01/anat/sub-01_hemi-R_thickness.shape.gii
smriprep/sub-01/anat/sub-01_hemi-R_white.surf.gii
smriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
smriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
smriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
smriprep/sub-01/anat/sub-01_space-fsLR_den-91k_curv.dscalar.nii
smriprep/sub-01/anat/sub-01_space-fsLR_den-91k_curv.json
smriprep/sub-01/anat/sub-01_space-fsLR_den-91k_sulc.dscalar.nii
smriprep/sub-01/anat/sub-01_space-fsLR_den-91k_sulc.json
smriprep/sub-01/anat/sub-01_space-fsLR_den-91k_thickness.dscalar.nii
smriprep/sub-01/anat/sub-01_space-fsLR_den-91k_thickness.json
smriprep/sub-01.html
/tmp/ds005/derivatives
1 change: 1 addition & 0 deletions .circleci/ds005_run.sh
Original file line number Diff line number Diff line change
Expand Up @@ -19,4 +19,5 @@ docker run -it -e FMRIPREP_DEV=1 -u $(id -u) \
--ncpus 2 --omp-nthreads 2 -vv \
--fs-license-file /tmp/fslicense/license.txt \
--fs-subjects-dir /tmp/ds005/freesurfer \
--cifti-output \
${@:1}
2 changes: 1 addition & 1 deletion .circleci/nipype.cfg
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
[execution]
stop_on_first_crash = true
poll_sleep_duration = 0.01
hash_method = content
hash_method = content
13 changes: 13 additions & 0 deletions .circleci/pytest.sh
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
#!/bin/bash
docker run --rm -it \
-v /tmp/data:/tmp/data:rw \
-v /tmp/fslicense:/tmp/fslicense:ro \
-v /tmp/templateflow:/home/smriprep/.cache/templateflow \
-v /tmp/src/smriprep/docker/multiproc.coveragerc:/tmp/multiproc.coveragerc:ro \
-v /tmp/src/smriprep/.circleci/nipype.cfg:/home/smriprep/.nipype/nipype.cfg \
-e FS_LICENSE=/tmp/fslicense/license.txt \
--entrypoint=pytest \
nipreps/smriprep:latest \
-v --doctest-modules --pyargs smriprep \
--cov smriprep --cov-report=xml:/tmp/data/pytest_cov.xml \
${@:1}
4 changes: 2 additions & 2 deletions .github/workflows/pythonpackage.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ on:
branches: [ '*' ]
tags: [ '*' ]
pull_request:
branches: [ master, 'maint/*' ]
branches: [ master, 'maint/*', 'next' ]
schedule:
- cron: '0 0 * * *'

Expand Down Expand Up @@ -65,7 +65,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.8, 3.9, "3.10", "3.11"]
python-version: ["3.10", "3.11"]
install: [repo]
include:
- python-version: "3.11"
Expand Down
2 changes: 1 addition & 1 deletion .gitignore
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Auto-generated by .maint/make_gitignore on Fri May 19 03:22:33 PM EDT 2023
# Auto-generated by .maint/make_gitignore on Wed Nov 8 04:05:04 PM EST 2023
# setuptools_scm
_version.py

Expand Down
4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
exclude: ".*/data/.*"
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
hooks:
- id: trailing-whitespace
exclude: .gitignore
exclude: '.gitignore|.*\.gii$'
- id: end-of-file-fixer
exclude: 'data/itkIdentityTransform.txt|\.svg$'
- id: check-yaml
- id: check-added-large-files
- id: check-toml
Expand Down
66 changes: 4 additions & 62 deletions Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -56,27 +56,6 @@ COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exc
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
| tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt

# AFNI
FROM downloader as afni
# Bump the date to current to update AFNI
RUN echo "2023.04.04"
RUN mkdir -p /opt/afni-latest \
&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C /opt/afni-latest --strip-components 1 \
--exclude "linux_openmp_64/*.gz" \
--exclude "linux_openmp_64/funstuff" \
--exclude "linux_openmp_64/shiny" \
--exclude "linux_openmp_64/afnipy" \
--exclude "linux_openmp_64/lib/RetroTS" \
--exclude "linux_openmp_64/lib_RetroTS" \
--exclude "linux_openmp_64/meica.libs" \
# Keep only what we use
&& find /opt/afni-latest -type f -not \( \
-name "3dTshift" -or \
-name "3dUnifize" -or \
-name "3dAutomask" -or \
-name "3dvolreg" \) -delete

# Connectome Workbench 1.5.0
FROM downloader as workbench
RUN mkdir /opt/workbench && \
Expand Down Expand Up @@ -115,56 +94,24 @@ ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"

# Some baseline tools; bc is needed for FreeSurfer, so don't drop it
# Some baseline tools
# bc is needed for FreeSurfer
# libglu1-mesa-dev is needed for Connectome Workbench
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RUN apt-get update && \
apt-get install -y --no-install-recommends \
bc \
ca-certificates \
curl \
git \
gnupg \
libglu1-mesa-dev \
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lsb-release \
netbase \
xvfb && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Configure PPAs for libpng12 and libxp6
RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
&& GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
&& echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
&& echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list

# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04)
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ed \
gsl-bin \
libglib2.0-0 \
libglu1-mesa-dev \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libpng12-0 \
libxm4 \
libxp6 \
netpbm \
tcsh \
xfonts-base \
xvfb \
&& curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \
&& dpkg -i /tmp/multiarch.deb \
&& rm /tmp/multiarch.deb \
&& apt-get install -f \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
&& if [ -n "$gsl2_path" ]; then \
ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
fi \
&& ldconfig

# Install files from stages
COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
COPY --from=afni /opt/afni-latest /opt/afni-latest
COPY --from=workbench /opt/workbench /opt/workbench

# Simulate SetUpFreeSurfer.sh
Expand All @@ -184,11 +131,6 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"

# AFNI config
ENV PATH="/opt/afni-latest:$PATH" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_PLUGINPATH="/opt/afni-latest"

# Workbench config
ENV PATH="/opt/workbench/bin_linux64:$PATH" \
LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
Expand Down
1 change: 0 additions & 1 deletion Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -15,4 +15,3 @@ docker:
--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
--build-arg VCS_REF=`git rev-parse --short HEAD` \
--build-arg VERSION=`python setup.py --version` .

4 changes: 2 additions & 2 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,15 @@ sMRIPrep: Structural MRI PREProcessing pipeline

.. image:: https://circleci.com/gh/nipreps/smriprep/tree/master.svg?style=shield
:target: https://circleci.com/gh/nipreps/smriprep/tree/master

.. image:: https://codecov.io/gh/nipreps/smriprep/branch/master/graph/badge.svg
:target: https://codecov.io/gh/nipreps/smriprep
:alt: Coverage report

.. image:: https://img.shields.io/pypi/v/smriprep.svg
:target: https://pypi.python.org/pypi/smriprep/
:alt: Latest Version

.. image:: https://img.shields.io/badge/doi-10.1038%2Fs41592--018--0235--4-blue.svg
:target: https://doi.org/10.1038/s41592-018-0235-4
:alt: Published in Nature Methods
Expand Down
2 changes: 1 addition & 1 deletion docs/_static/alabaster.css
Original file line number Diff line number Diff line change
Expand Up @@ -698,4 +698,4 @@ nav#breadcrumbs li+li:before {
div.related {
display: none;
}
}
}
2 changes: 1 addition & 1 deletion docs/_static/basic.css
Original file line number Diff line number Diff line change
Expand Up @@ -673,4 +673,4 @@ div.math:hover a.headerlink {
#top-link {
display: none;
}
}
}
2 changes: 1 addition & 1 deletion docs/_static/documentation_options.js
Original file line number Diff line number Diff line change
Expand Up @@ -7,4 +7,4 @@ var DOCUMENTATION_OPTIONS = {
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
NAVIGATION_WITH_KEYS: false,
};
};
4 changes: 1 addition & 3 deletions docs/_static/language_data.js
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];


/* Non-minified version JS is _stemmer.js if file is provided */
/* Non-minified version JS is _stemmer.js if file is provided */
/**
* Porter Stemmer
*/
Expand Down Expand Up @@ -293,5 +293,3 @@ function splitQuery(query) {
}
return result;
}


2 changes: 1 addition & 1 deletion docs/_static/pygments.css
Original file line number Diff line number Diff line change
Expand Up @@ -74,4 +74,4 @@
.highlight .vg { color: #000000 } /* Name.Variable.Global */
.highlight .vi { color: #000000 } /* Name.Variable.Instance */
.highlight .vm { color: #000000 } /* Name.Variable.Magic */
.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */
.highlight .il { color: #990000 } /* Literal.Number.Integer.Long */
1 change: 0 additions & 1 deletion docs/_templates/apidoc/module.rst_t
Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,3 @@
{%- for option in automodule_options %}
:{{ option }}:
{%- endfor %}

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