diff --git a/.dockerignore b/.dockerignore
index eb58af287ce..9fdac0a3b14 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -12,7 +12,3 @@ fmriprep.egg-info/**/*
 fmriprep.egg-info
 .eggs/**/*
 .eggs
-
-.venv
-.pixi
-.tox
diff --git a/Dockerfile b/Dockerfile
index d52726ddf17..e71f9f29de9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,79 +22,226 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-ARG BASE_IMAGE=ghcr.io/nipreps/fmriprep-base:20251006
+# Ubuntu 22.04 LTS - Jammy
+ARG BASE_IMAGE=ubuntu:jammy-20240125
 
 #
-# Build pixi environment
-# The Pixi environment includes:
-#   - Python
-#     - Scientific Python stack (via conda-forge)
-#     - General Python dependencies (via PyPI)
-#   - FSL (via fslconda)
-#   - ants (via conda-forge)
-#   - connectome-workbench (via conda-forge)
-#   - ...
+# Build wheel
 #
-FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build
+FROM python:slim AS src
+RUN pip install build
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends git
+COPY . /src
+RUN python -m build /src
+
+#
+# Download stages
+#
+
+# Utilities for downloading packages
+FROM ${BASE_IMAGE} as downloader
+# Bump the date to current to refresh curl/certificates/etc
+RUN echo "2024.03.08"
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
+                    binutils \
+                    bzip2 \
                     ca-certificates \
-                    git && \
+                    curl \
+                    unzip && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-# Run post-link scripts during install, but use global to keep out of source tree
-RUN pixi config set --global run-post-link-scripts insecure
-
-# Install dependencies before the package itself to leverage caching
-RUN mkdir /app
-COPY pixi.lock pyproject.toml /app
-WORKDIR /app
-RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e niworkflows -e test --frozen --skip niworkflows
-# Note that PATH gets hard-coded. Remove it and re-apply in final image
-RUN pixi shell-hook -e niworkflows --as-is | grep -v PATH > /shell-hook.sh
-RUN pixi shell-hook -e test --as-is | grep -v PATH > /test-shell-hook.sh
-
-# Finally, install the package
-COPY . /app
-RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e niworkflows -e test --frozen
 
-#
-# Pre-fetch templates
-#
-FROM ghcr.io/astral-sh/uv:python3.12-alpine AS templates
-ENV TEMPLATEFLOW_HOME="/templateflow"
-RUN uv pip install --system templateflow
-COPY docker/fetch_templates.py fetch_templates.py
-RUN python fetch_templates.py
+# FreeSurfer 7.3.2
+FROM downloader as freesurfer
+COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt
+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 "2024.03.08"
+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
+
+# Micromamba
+FROM downloader as micromamba
+
+# Install a C compiler to build extensions when needed.
+# traits<6.4 wheels are not available for Python 3.11+, but build easily.
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+WORKDIR /
+# Bump the date to current to force update micromamba
+RUN echo "2024.03.08"
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+COPY env.yml /tmp/env.yml
+COPY requirements.txt /tmp/requirements.txt
+WORKDIR /tmp
+RUN micromamba create -y -f /tmp/env.yml && \
+    micromamba clean -y -a
 
 #
 # Main stage
 #
-FROM ${BASE_IMAGE} AS base
+FROM ${BASE_IMAGE} as main
+
+# Configure apt
+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
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    bc \
+                    ca-certificates \
+                    curl \
+                    git \
+                    gnupg \
+                    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 $gsl2_path)/libgsl.so.0"; \
+    fi \
+    && ldconfig
+
+# Install files from stages
+COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
+COPY --from=afni /opt/afni-latest /opt/afni-latest
+
+# Simulate SetUpFreeSurfer.sh
+ENV OS="Linux" \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA="" \
+    FSF_OUTPUT_FORMAT="nii.gz" \
+    FREESURFER_HOME="/opt/freesurfer"
+ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
+    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
+    MNI_DIR="$FREESURFER_HOME/mni" \
+    LOCAL_DIR="$FREESURFER_HOME/local" \
+    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
+    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
+    MNI_DATAPATH="$FREESURFER_HOME/mni/data"
+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"
 
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users niworkflows
 WORKDIR /home/niworkflows
-ENV HOME="/home/niworkflows"
-
-COPY --link --from=templates /templateflow /home/fmriprep/.cache/templateflow
-
-RUN chmod -R go=u $HOME
+ENV HOME="/home/niworkflows" \
+    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+
+COPY --from=micromamba /bin/micromamba /bin/micromamba
+COPY --from=micromamba /opt/conda/envs/niworkflows /opt/conda/envs/niworkflows
+
+ENV MAMBA_ROOT_PREFIX="/opt/conda"
+RUN micromamba shell init -s bash && \
+    echo "micromamba activate niworkflows" >> $HOME/.bashrc
+ENV PATH="/opt/conda/envs/niworkflows/bin:$PATH" \
+    CPATH="/opt/conda/envs/niworkflows/include:$CPATH" \
+    LD_LIBRARY_PATH="/opt/conda/envs/niworkflows/lib:$LD_LIBRARY_PATH"
+
+COPY docker/fetch_templates.py /tmp/fetch_templates.py
+RUN python /tmp/fetch_templates.py && \
+    rm /tmp/fetch_templates.py && \
+    find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
+    find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
+
+# FSL environment
+ENV LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1 \
+    FSLDIR="/opt/conda/envs/fmriprep" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q"
 
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
-COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
-
-WORKDIR /tmp
+# Installing niworkflows
+COPY --from=src /src/dist/*.whl .
+RUN pip install --no-cache-dir $( ls *.whl )[all]
 
-FROM base AS test
+COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
 
-COPY --link --from=build /app/.pixi/envs/test /app/.pixi/envs/test
-COPY --link --from=build /test-shell-hook.sh /shell-hook.sh
-RUN cat /shell-hook.sh >> $HOME/.bashrc
-ENV PATH="/app/.pixi/envs/test/bin:$PATH"
+# Cleanup and ensure perms.
+RUN rm -rf $HOME/.npm $HOME/.conda $HOME/.empty && \
+    find $HOME -type d -exec chmod go=u {} + && \
+    find $HOME -type f -exec chmod go=u {} +
 
-ENV FSLDIR="/app/.pixi/envs/test"
+# Final settings
+WORKDIR /tmp
+ARG BUILD_DATE
+ARG VCS_REF
+LABEL org.label-schema.build-date=$BUILD_DATE \
+      org.label-schema.name="niworkflows" \
+      org.label-schema.description="niworkflows - NeuroImaging workflows" \
+      org.label-schema.url="https://github.com/nipreps/niworkflows" \
+      org.label-schema.vcs-ref=$VCS_REF \
+      org.label-schema.vcs-url="https://github.com/nipreps/niworkflows" \
+      org.label-schema.version=$VERSION \
+      org.label-schema.schema-version="1.0"
diff --git a/env.yml b/env.yml
new file mode 100644
index 00000000000..389ebfbb95c
--- /dev/null
+++ b/env.yml
@@ -0,0 +1,36 @@
+name: niworkflows
+channels:
+  - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+  - conda-forge
+# Update this ~yearly; last updated Mar 2025
+dependencies:
+  - python=3.12
+  # Intel Math Kernel Library for numpy
+  - mkl=2024.2.2
+  - mkl-service=2.4.2
+  # Base scientific python stack; required by FSL, so pinned here
+  - numpy=1.26
+  - scipy=1.15
+  - matplotlib=3.9
+  - pandas=2.2
+  - h5py=3.13
+  # Dependencies compiled against numpy, best to stick with conda
+  - scikit-image=0.25
+  - scikit-learn=1.6
+  # Utilities
+  - graphviz=11.0
+  # Workflow dependencies: ANTs
+  - ants=2.5
+  # 5.4.1 and 5.4.2 cause segfaults with ants
+  # Try to remove this ASAP
+  # https://github.com/conda-forge/ants-feedstock/issues/19
+  - libitk=5.4.0
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.13)
+  - fsl-bet2=2111.8
+  - fsl-flirt=2111.2
+  - fsl-fast4=2111.3
+  - fsl-mcflirt=2111.0
+  - fsl-miscmaths=2203.2
+  - pip
+  - pip:
+    - -r requirements.txt
diff --git a/pixi.lock b/pixi.lock
deleted file mode 100644
index 37a5d1abc53..00000000000
--- a/pixi.lock
+++ /dev/null
@@ -1,5360 +0,0 @@
-version: 6
-environments:
-  default:
-    channels:
-    - url: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
-    - url: https://conda.anaconda.org/conda-forge/
-    indexes:
-    - https://pypi.org/simple
-    packages:
-      linux-64:
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-5_kmp_llvm.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/ants-2.5.4-h8c3795b_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-h39aace5_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.5-hc2324a3_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb03c661_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb03c661_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/brunsli-0.1-he3183e4_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.14.4-hb4ffafa_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/certifi-2025.10.5-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/charls-2.4.2-h59595ed_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.3-py312hd9148b4_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/dbus-1.13.6-h5008d03_3.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/dill-0.4.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h171cf75_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.1-hecca717_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hf1063bd_110.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.60.1-py312h8a5da7c_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.16-hb03c661_0.conda
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-armawrap-0.7.0-hdef71a4_1.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-avwutils-2209.3-hb6de94e_0.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/noarch/fsl-base-2508.1-py_0.conda
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-basisfield-2203.1-hb6de94e_7.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-bet2-2111.8-hb6de94e_0.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-cprob-2111.0-hdef71a4_6.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-fast4-2111.3-hb6de94e_3.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-flirt-2111.2-hb6de94e_3.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-fnirt-2203.1-hb6de94e_0.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-fugue-2201.5-hb6de94e_0.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/noarch/fsl-installer-3.17.0-py_0.conda
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-mcflirt-2111.0-hb6de94e_6.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-meshclass-2111.0-hb6de94e_7.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-misc_c-2111.0-hdef71a4_6.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/noarch/fsl-misc_tcl-2406.0-0.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-miscmaths-2203.2-hb6de94e_5.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-newimage-2203.12-h489b204_0.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-newnifti-4.1.0-hdef71a4_5.tar.bz2
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/noarch/fsl-sub-2.10.0-py_0.conda
-      - conda: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/linux-64/fsl-utils-2203.5-hb6de94e_0.tar.bz2
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-  size: 96433
-  timestamp: 1749230076687
-- conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda
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-  depends:
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-  - __glibc >=2.17,<3.0.a0
-  license: MIT
-  license_family: MIT
-  purls: []
-  size: 85189
-  timestamp: 1753484064210
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zfp-1.0.1-h909a3a2_3.conda
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-  - __glibc >=2.17,<3.0.a0
-  - _openmp_mutex >=4.5
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-  license: BSD-3-Clause
-  license_family: BSD
-  purls: []
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-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhd8ed1ab_0.conda
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-  size: 22963
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h4ab18f5_6.conda
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-ng-2.0.7-h0b41bf4_0.conda
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diff --git a/pyproject.toml b/pyproject.toml
index dcebed108d6..513dbecd48a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -231,9 +231,12 @@ ignore-words-list = "objekt,nd"
 channels = ["https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public", "conda-forge"]
 platforms = ["linux-64"]
 
-[tool.pixi.activation.env]
+[tool.pixi.feature.niworkflows.activation.env]
 FSLDIR = "$CONDA_PREFIX"
 
+[tool.pixi.pypi-dependencies]
+niworkflows = { path = ".", editable = true }
+
 [tool.pixi.environments]
 default = { features = ["editable"], solve-group = "default" }
 test = { features = ["editable", "tests"], solve-group = "default" }
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000000..7dcb1e07407
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,243 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --strip-extras pyproject.toml -o requirements.txt -p 3.12 -c-
+acres==0.3.0
+    # via
+    #   niworkflows (pyproject.toml)
+    #   nipype
+attrs==25.1.0
+    # via
+    #   niworkflows (pyproject.toml)
+    #   jsonschema
+    #   referencing
+bids-validator==1.14.7.post0
+    # via pybids
+bidsschematools==1.0.3
+    # via bids-validator
+certifi==2025.1.31
+    # via requests
+charset-normalizer==3.4.1
+    # via requests
+ci-info==0.3.0
+    # via etelemetry
+click==8.1.8
+    # via
+    #   bidsschematools
+    #   nipype
+    #   pybids
+contourpy==1.3.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+docopt==0.6.2
+    # via num2words
+etelemetry==0.3.1
+    # via nipype
+filelock==3.17.0
+    # via nipype
+fonttools==4.56.0
+    # via matplotlib
+formulaic==1.1.1
+    # via pybids
+frozendict==2.4.6
+    # via pybids
+fsspec==2025.2.0
+    # via universal-pathlib
+greenlet==3.1.1
+    # via sqlalchemy
+h5py==3.13.0
+    # via nitransforms
+idna==3.10
+    # via requests
+imageio==2.37.0
+    # via scikit-image
+interface-meta==1.3.0
+    # via formulaic
+isodate==0.6.1
+    # via rdflib
+jinja2==3.1.6
+    # via niworkflows (pyproject.toml)
+joblib==1.4.2
+    # via
+    #   nilearn
+    #   scikit-learn
+jsonschema==4.23.0
+    # via bidsschematools
+jsonschema-specifications==2024.10.1
+    # via jsonschema
+kiwisolver==1.4.8
+    # via matplotlib
+lazy-loader==0.4
+    # via scikit-image
+looseversion==1.3.0
+    # via
+    #   niworkflows (pyproject.toml)
+    #   nipype
+lxml==5.3.1
+    # via
+    #   nilearn
+    #   prov
+    #   svgutils
+markupsafe==3.0.2
+    # via jinja2
+matplotlib==3.9.4
+    # via
+    #   niworkflows (pyproject.toml)
+    #   seaborn
+networkx==3.4.2
+    # via
+    #   nipype
+    #   prov
+    #   scikit-image
+nibabel==5.3.2
+    # via
+    #   niworkflows (pyproject.toml)
+    #   nilearn
+    #   nipype
+    #   nitransforms
+    #   pybids
+nilearn==0.11.1
+    # via niworkflows (pyproject.toml)
+nipype==1.9.2
+    # via niworkflows (pyproject.toml)
+nitransforms==24.1.1
+    # via niworkflows (pyproject.toml)
+num2words==0.5.14
+    # via pybids
+numpy==1.26.4
+    # via
+    #   niworkflows (pyproject.toml)
+    #   contourpy
+    #   formulaic
+    #   h5py
+    #   imageio
+    #   matplotlib
+    #   nibabel
+    #   nilearn
+    #   nipype
+    #   nitransforms
+    #   pandas
+    #   pybids
+    #   scikit-image
+    #   scikit-learn
+    #   scipy
+    #   seaborn
+    #   tifffile
+    #   transforms3d
+packaging==24.2
+    # via
+    #   niworkflows (pyproject.toml)
+    #   etelemetry
+    #   lazy-loader
+    #   matplotlib
+    #   nibabel
+    #   nilearn
+    #   nipype
+    #   scikit-image
+pandas==2.2.3
+    # via
+    #   niworkflows (pyproject.toml)
+    #   formulaic
+    #   nilearn
+    #   pybids
+    #   seaborn
+pillow==11.1.0
+    # via
+    #   imageio
+    #   matplotlib
+    #   scikit-image
+prov==2.0.1
+    # via nipype
+puremagic==1.28
+    # via nipype
+pybids==0.19.0
+    # via
+    #   niworkflows (pyproject.toml)
+    #   templateflow
+pydot==3.0.4
+    # via nipype
+pyparsing==3.2.1
+    # via
+    #   matplotlib
+    #   pydot
+    #   rdflib
+python-dateutil==2.9.0.post0
+    # via
+    #   matplotlib
+    #   nipype
+    #   pandas
+    #   prov
+pytz==2025.1
+    # via pandas
+pyyaml==6.0.2
+    # via
+    #   niworkflows (pyproject.toml)
+    #   bidsschematools
+rdflib==6.3.2
+    # via
+    #   nipype
+    #   prov
+referencing==0.36.2
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+requests==2.32.4
+    # via
+    #   etelemetry
+    #   nilearn
+    #   templateflow
+rpds-py==0.23.1
+    # via
+    #   jsonschema
+    #   referencing
+scikit-image==0.25.2
+    # via niworkflows (pyproject.toml)
+scikit-learn==1.6.1
+    # via nilearn
+scipy==1.15.2
+    # via
+    #   niworkflows (pyproject.toml)
+    #   formulaic
+    #   nilearn
+    #   nipype
+    #   nitransforms
+    #   pybids
+    #   scikit-image
+    #   scikit-learn
+seaborn==0.13.2
+    # via niworkflows (pyproject.toml)
+simplejson==3.20.1
+    # via nipype
+six==1.17.0
+    # via
+    #   isodate
+    #   python-dateutil
+sqlalchemy==2.0.38
+    # via pybids
+svgutils==0.3.4
+    # via niworkflows (pyproject.toml)
+templateflow==24.2.2
+    # via niworkflows (pyproject.toml)
+threadpoolctl==3.5.0
+    # via scikit-learn
+tifffile==2025.2.18
+    # via scikit-image
+tqdm==4.67.1
+    # via templateflow
+traits==7.0.2
+    # via nipype
+transforms3d==0.4.2
+    # via niworkflows (pyproject.toml)
+typing-extensions==4.12.2
+    # via
+    #   formulaic
+    #   nibabel
+    #   referencing
+    #   sqlalchemy
+tzdata==2025.1
+    # via pandas
+universal-pathlib==0.2.6
+    # via pybids
+urllib3==2.5.0
+    # via requests
+wrapt==1.17.2
+    # via formulaic