sMRIPrep 0.13

.circleci/config.yml

@@ -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
@@ -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:
@@ -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
@@ -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
@@ -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
       - restore_cache:
           keys:
             - testdata-v2-{{ .Branch }}-{{ epoch }}
@@ -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
 
@@ -772,8 +799,6 @@ workflows:
               only: /.*/
 
       - get_data:
-          context:
-            - fs-license
           filters:
             branches:
               ignore:
@@ -793,10 +818,11 @@ workflows:
             tags:
               only: /.*/
 
-      - test_wrapper:
+      - test:
           context:
             - nipreps-common
           requires:
+            - get_data
             - build
           filters:
             branches:
@@ -852,7 +878,7 @@ workflows:
             - build_docs
             - ds005
             - ds054
-            - test_wrapper
+            - test
           filters:
             branches:
               only: /master/
@@ -865,7 +891,7 @@ workflows:
             - ds005
             - ds054
             - test_deploy_pypi
-            - test_wrapper
+            - test
           filters:
             branches:
               ignore: /.*/

.circleci/ds005_outputs.txt

@@ -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
@@ -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
@@ -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

.circleci/ds005_run.sh

@@ -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}

.circleci/nipype.cfg

@@ -1,4 +1,4 @@
 [execution]
 stop_on_first_crash = true
 poll_sleep_duration = 0.01
-hash_method = content
+hash_method = content

.circleci/pytest.sh

@@ -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}

.github/workflows/pythonpackage.yml

@@ -5,7 +5,7 @@ on:
     branches: [ '*' ]
     tags: [ '*' ]
   pull_request:
-    branches: [ master, 'maint/*' ]
+    branches: [ master, 'maint/*', 'next' ]
   schedule:
     - cron: '0 0 * * *'
 
@@ -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"

.gitignore

@@ -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
 

.pre-commit-config.yaml

@@ -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

Dockerfile

@@ -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 && \
@@ -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 is needed for Connectome Workbench
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     bc \
                     ca-certificates \
                     curl \
                     git \
                     gnupg \
+                    libglu1-mesa \
                     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
@@ -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"

Makefile

@@ -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` .
-

README.rst

@@ -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

docs/_static/alabaster.css

@@ -698,4 +698,4 @@ nav#breadcrumbs li+li:before {
     div.related {
         display: none;
     }
-}
+}

docs/_static/basic.css

@@ -673,4 +673,4 @@ div.math:hover a.headerlink {
     #top-link {
         display: none;
     }
-}
+}

docs/_static/documentation_options.js

@@ -7,4 +7,4 @@ var DOCUMENTATION_OPTIONS = {
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',
     NAVIGATION_WITH_KEYS: false,
-};
+};

docs/_static/language_data.js

@@ -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
  */
@@ -293,5 +293,3 @@ function splitQuery(query) {
     }
     return result;
 }
-
-

docs/_static/pygments.css

@@ -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 */

docs/_templates/apidoc/module.rst_t

@@ -6,4 +6,3 @@
 {%- for option in automodule_options %}
    :{{ option }}:
 {%- endfor %}
-