diff --git a/Dockerfile b/Dockerfile
index 87c5b39fc..3f37fb086 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -23,17 +23,17 @@
 # SOFTWARE.
 
 # Ubuntu 22.04 LTS - Jammy
-ARG BASE_IMAGE=ubuntu:jammy-20230308
+ARG BASE_IMAGE=ubuntu:jammy-20240125
 
 #
-# fMRIPrep wheel
+# Build wheel
 #
 FROM python:slim AS src
 RUN pip install build
 RUN apt-get update && \
     apt-get install -y --no-install-recommends git
-COPY . /src/fmriprep
-RUN python -m build /src/fmriprep
+COPY . /src
+RUN python -m build /src
 
 #
 # Download stages
@@ -96,9 +96,16 @@ RUN mkdir /opt/convert3d && \
 
 # 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 "2023.04.05"
+RUN echo "2024.02.06"
 RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
 ENV MAMBA_ROOT_PREFIX="/opt/conda"
@@ -112,7 +119,7 @@ RUN micromamba create -y -f /tmp/env.yml && \
 # Check if this is still necessary when updating the base image.
 ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH" \
     UV_USE_IO_URING=0
-RUN npm install -g svgo@^3.0.4 bids-validator@^1.13.1 && \
+RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \
     rm -r ~/.npm
 
 #
@@ -249,7 +256,7 @@ RUN curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/e
     && chmod +x /usr/local/bin/msm
 
 # Installing FMRIPREP
-COPY --from=src /src/fmriprep/dist/*.whl .
+COPY --from=src /src/dist/*.whl .
 RUN pip install --no-cache-dir $( ls *.whl )[container,test]
 
 RUN find $HOME -type d -exec chmod go=u {} + && \
diff --git a/docs/installation.rst b/docs/installation.rst
index 5420d1427..a812fcf30 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -85,12 +85,12 @@ nipype_.
 not handled by the Python's packaging system (Pypi) used to deploy
 the ``fmriprep`` package:
 
-- FSL_ (version 6.0.6.2)
-- ANTs_ (version 2.4.4)
-- AFNI_ (version 23.1.05)
-- `C3D <https://sourceforge.net/projects/c3d/>`_ (version 1.3.0)
+- FSL_ (version 6.0.7.7)
+- ANTs_ (version 2.5.1)
+- AFNI_ (version 24.0.05)
+- `C3D <https://sourceforge.net/projects/c3d/>`_ (version 1.4.0)
 - FreeSurfer_ (version 7.3.2)
-- `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.8.0)
+- `bids-validator <https://github.com/bids-standard/bids-validator>`_ (version 1.14.0)
 - `connectome-workbench <https://www.humanconnectome.org/software/connectome-workbench>`_ (version 1.5.0)
 
 Not running on a local machine? - Data transfer
diff --git a/env.yml b/env.yml
index ac9bc2e9b..b5e0a33d8 100644
--- a/env.yml
+++ b/env.yml
@@ -2,36 +2,36 @@ name: fmriprep
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-# Update this ~yearly; last updated April 2023
+# Update this ~yearly; last updated Jan 2024
 dependencies:
-  - python=3.10
+  - python=3.11
   # Needed for svgo and bids-validator; consider moving to deno
-  - nodejs=18
+  - nodejs=20
   # Intel Math Kernel Library for numpy
-  - mkl=2022.1
-  - mkl-service=2.4
+  - mkl=2023.2.0
+  - mkl-service=2.4.0
   # git-annex for templateflow users with DataLad superdatasets
   - git-annex=*=alldep*
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
   - scipy=1.11
   - matplotlib=3.8
-  - pandas=2.1
+  - pandas=2.2
   - h5py=3.10
   # Dependencies compiled against numpy, best to stick with conda
   - nitime=0.10
   - scikit-image=0.22
-  - scikit-learn=1.3
+  - scikit-learn=1.4
   # Utilities
-  - graphviz=6.0
+  - graphviz=9.0
   - pandoc=3.1
   # Workflow dependencies: ANTs
-  - ants=2.5.0
-  # Workflow dependencies: FSL (versions pinned in 6.0.7.4)
+  - ants=2.5
+  # Workflow dependencies: FSL (versions pinned in 6.0.7.7)
   - fsl-bet2=2111.4
   - fsl-flirt=2111.2
   - fsl-fast4=2111.3
-  - fsl-fugue=2201.3
+  - fsl-fugue=2201.4
   - fsl-mcflirt=2111.0
   - fsl-miscmaths=2203.2
   - fsl-topup=2203.2
diff --git a/requirements.txt b/requirements.txt
index 60ea70687..dd51ea4d6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -17,17 +17,17 @@ arrow==1.3.0
     # via codecarbon
 astor==0.8.1
     # via formulaic
-attrs==23.1.0
+attrs==23.2.0
     # via
     #   niworkflows
     #   sdcflows
-bids-validator==1.13.1
+bids-validator==1.14.0
     # via pybids
-bokeh==3.3.1
+bokeh==3.3.4
     # via tedana
 boto==2.49.0
     # via datalad
-certifi==2023.11.17
+certifi==2024.2.2
     # via
     #   requests
     #   sentry-sdk
@@ -46,7 +46,7 @@ click==8.1.7
     #   codecarbon
     #   nipype
     #   pybids
-codecarbon==2.3.1
+codecarbon==2.3.4
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -54,20 +54,20 @@ contourpy==1.2.0
     # via
     #   bokeh
     #   matplotlib
-cryptography==41.0.7
+cryptography==42.0.2
     # via secretstorage
 cycler==0.12.1
     # via matplotlib
-datalad==0.19.4
+datalad==0.19.6
     # via
     #   datalad-next
     #   datalad-osf
     #   fmriprep (pyproject.toml)
-datalad-next==1.0.2
+datalad-next==1.2.0
     # via datalad-osf
 datalad-osf==0.3.0
     # via fmriprep (pyproject.toml)
-distro==1.8.0
+distro==1.9.0
     # via datalad
 docopt==0.6.2
     # via num2words
@@ -77,13 +77,11 @@ fasteners==0.19
     # via datalad
 filelock==3.13.1
     # via nipype
-fonttools==4.45.0
+fonttools==4.48.1
     # via matplotlib
 formulaic==0.5.2
     # via pybids
-fuzzywuzzy==0.18.0
-    # via codecarbon
-greenlet==3.0.1
+greenlet==3.0.3
     # via sqlalchemy
 h5py==3.10.0
     # via nitransforms
@@ -91,11 +89,11 @@ humanize==4.9.0
     # via
     #   datalad
     #   datalad-next
-idna==3.4
+idna==3.6
     # via requests
-imageio==2.33.0
+imageio==2.33.1
     # via scikit-image
-importlib-metadata==7.0.0
+importlib-metadata==7.0.1
     # via keyring
 importlib-resources==6.1.1
     # via
@@ -118,7 +116,7 @@ jeepney==0.8.0
     # via
     #   keyring
     #   secretstorage
-jinja2==3.1.2
+jinja2==3.1.3
     # via
     #   bokeh
     #   niworkflows
@@ -144,14 +142,14 @@ looseversion==1.3.0
     #   nipype
     #   niworkflows
     #   smriprep
-lxml==4.9.3
+lxml==5.1.0
     # via
     #   nilearn
     #   prov
     #   svgutils
 mapca==0.0.4
     # via tedana
-markupsafe==2.1.3
+markupsafe==2.1.5
     # via jinja2
 matplotlib==3.8.2
     # via
@@ -165,8 +163,10 @@ migas==0.4.0
     # via
     #   fmriprep
     #   sdcflows
-more-itertools==10.1.0
-    # via jaraco-classes
+more-itertools==10.2.0
+    # via
+    #   datalad-next
+    #   jaraco-classes
 msgpack==1.0.7
     # via datalad
 networkx==3.2.1
@@ -174,7 +174,7 @@ networkx==3.2.1
     #   nipype
     #   prov
     #   scikit-image
-nibabel==5.1.0
+nibabel==5.2.0
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
@@ -188,7 +188,7 @@ nibabel==5.1.0
     #   sdcflows
     #   smriprep
     #   tedana
-nilearn==0.10.2
+nilearn==0.10.3
     # via
     #   mapca
     #   nireports
@@ -224,7 +224,7 @@ niworkflows==1.10.0
     #   smriprep
 num2words==0.5.13
     # via pybids
-numpy==1.26.2
+numpy==1.26.4
     # via
     #   bokeh
     #   contourpy
@@ -268,7 +268,7 @@ packaging==23.2
     #   niworkflows
     #   scikit-image
     #   smriprep
-pandas==2.1.3
+pandas==2.2.0
     # via
     #   bokeh
     #   codecarbon
@@ -281,21 +281,21 @@ pandas==2.1.3
     #   pybids
     #   seaborn
     #   tedana
-patool==2.0.0
+patool==2.1.1
     # via datalad
-pillow==10.1.0
+pillow==10.2.0
     # via
     #   bokeh
     #   imageio
     #   matplotlib
     #   scikit-image
-platformdirs==4.1.0
+platformdirs==4.2.0
     # via datalad
 prometheus-client==0.19.0
     # via codecarbon
 prov==2.0.0
     # via nipype
-psutil==5.9.6
+psutil==5.9.8
     # via
     #   codecarbon
     #   fmriprep
@@ -313,7 +313,7 @@ pybids==0.16.4
     #   templateflow
 pycparser==2.21
     # via cffi
-pydot==1.4.2
+pydot==2.0.0
     # via nipype
 pynvml==11.5.0
     # via codecarbon
@@ -329,9 +329,9 @@ python-dateutil==2.8.2
     #   nipype
     #   pandas
     #   prov
-python-gitlab==4.2.0
+python-gitlab==4.4.0
     # via datalad
-pytz==2023.3.post1
+pytz==2024.1
     # via
     #   apscheduler
     #   pandas
@@ -341,6 +341,8 @@ pyyaml==6.0.1
     #   nireports
     #   niworkflows
     #   smriprep
+rapidfuzz==3.6.1
+    # via codecarbon
 rdflib==7.0.0
     # via
     #   nipype
@@ -363,7 +365,7 @@ scikit-image==0.22.0
     # via
     #   niworkflows
     #   sdcflows
-scikit-learn==1.3.2
+scikit-learn==1.4.0
     # via
     #   mapca
     #   nilearn
@@ -386,13 +388,13 @@ sdcflows==2.8.0
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-seaborn==0.13.0
+seaborn==0.13.2
     # via
     #   nireports
     #   niworkflows
 secretstorage==3.3.3
     # via keyring
-sentry-sdk==1.39.0
+sentry-sdk==1.40.1
     # via fmriprep
 simplejson==3.19.2
     # via nipype
@@ -406,7 +408,7 @@ smriprep==0.13.2
     # via
     #   fmriprep
     #   fmriprep (pyproject.toml)
-sqlalchemy==2.0.23
+sqlalchemy==2.0.25
     # via pybids
 svgutils==0.3.4
     # via
@@ -428,13 +430,14 @@ threadpoolctl==3.2.0
     # via
     #   scikit-learn
     #   tedana
-tifffile==2023.9.26
+tifffile==2024.1.30
     # via scikit-image
 toml==0.10.2
     # via
     #   fmriprep
+    #   fmriprep (pyproject.toml)
     #   sdcflows
-tornado==6.3.3
+tornado==6.4
     # via bokeh
 tqdm==4.66.1
     # via
@@ -448,18 +451,18 @@ traits==6.3.2
     #   sdcflows
 transforms3d==0.4.1
     # via niworkflows
-types-python-dateutil==2.8.19.14
+types-python-dateutil==2.8.19.20240106
     # via arrow
-typing-extensions==4.8.0
+typing-extensions==4.9.0
     # via
     #   datalad
     #   formulaic
     #   sqlalchemy
-tzdata==2023.3
+tzdata==2023.4
     # via pandas
 tzlocal==5.2
     # via apscheduler
-urllib3==2.1.0
+urllib3==2.2.0
     # via
     #   requests
     #   sentry-sdk