diff --git a/.github/workflows/run_precommit.yml b/.github/workflows/run_precommit.yml
index a100dcb..65947d3 100644
--- a/.github/workflows/run_precommit.yml
+++ b/.github/workflows/run_precommit.yml
@@ -11,4 +11,4 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
-    - uses: pre-commit/action@v3.0.0
+    - uses: pre-commit/action@v3.0.1
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 735a460..1b7db23 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -46,7 +46,7 @@ jobs:
     - uses: actions/setup-python@v5
     - name: install tox
       run: pip install tox
-    - uses: actions/cache@v3
+    - uses: actions/cache@v4
       id: cache
       env:
         cache-name: ds000017
@@ -136,7 +136,7 @@ jobs:
 
     - name: Restore cached data ds000017
       id: cache
-      uses: actions/cache/restore@v3
+      uses: actions/cache/restore@v4
       with:
         path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
         key: ds000017
@@ -155,7 +155,7 @@ jobs:
       if: ${{ contains(needs.check_skip_flags.outputs.head-commit-message, 'full_test') }} || ${{ github.event.pull_request.merged }}
       run: pytest --cov=giga_connectome --cov-report=xml --doctest-modules -v --pyargs giga_connectome
 
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
       if: ${{ always() }}
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
@@ -176,7 +176,7 @@ jobs:
 
       - name: Restore cached data ds000017
         id: cache
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: /home/runner/work/giga_connectome/giga_connectome/giga_connectome/data/test_data
           key: ds000017
diff --git a/.github/workflows/update_precommit_hooks.yml b/.github/workflows/update_precommit_hooks.yml
index a0cf4bf..cdacc3c 100644
--- a/.github/workflows/update_precommit_hooks.yml
+++ b/.github/workflows/update_precommit_hooks.yml
@@ -43,7 +43,7 @@ jobs:
         -   name: Update pre-commit hooks
             run: pre-commit autoupdate
         -   name: Create Pull Request
-            uses: peter-evans/create-pull-request@v5
+            uses: peter-evans/create-pull-request@v6
             with:
                 commit-message: pre-commit hooks auto-update
                 base: main
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index faf8fab..9b63cd7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.3.0
     hooks:
     -   id: black
 -   repo: https://github.com/codespell-project/codespell
diff --git a/giga_connectome/logger.py b/giga_connectome/logger.py
index e859451..6a9e9b2 100644
--- a/giga_connectome/logger.py
+++ b/giga_connectome/logger.py
@@ -1,4 +1,5 @@
 """General logger for the cohort_creator package."""
+
 from __future__ import annotations
 
 import logging
diff --git a/giga_connectome/methods.py b/giga_connectome/methods.py
index 85150fc..84e6863 100644
--- a/giga_connectome/methods.py
+++ b/giga_connectome/methods.py
@@ -39,9 +39,9 @@ def generate_method_section(
         "atlas": atlas,
         "smoothing_fwhm": smoothing_fwhm,
         "strategy": strategy,
-        "standardize": "percent signal change"
-        if standardize == "psc"
-        else standardize,
+        "standardize": (
+            "percent signal change" if standardize == "psc" else standardize
+        ),
         "mni_space": mni_space,
         "average_correlation": average_correlation,
         "analysis_level": analysis_level,
diff --git a/giga_connectome/tests/test_cli.py b/giga_connectome/tests/test_cli.py
index 710ed08..fead8b5 100644
--- a/giga_connectome/tests/test_cli.py
+++ b/giga_connectome/tests/test_cli.py
@@ -1,6 +1,7 @@
 """
 Simple code to smoke test the functionality.
 """
+
 from pathlib import Path
 from pkg_resources import resource_filename
 from giga_connectome.run import main
diff --git a/giga_connectome/utils.py b/giga_connectome/utils.py
index 6cc38c0..0949abb 100644
--- a/giga_connectome/utils.py
+++ b/giga_connectome/utils.py
@@ -101,9 +101,11 @@ def _filter_pybids_none_any(dct: dict) -> dict:
     import bids
 
     return {
-        k: bids.layout.Query.NONE
-        if v is None
-        else (bids.layout.Query.ANY if v == "*" else v)
+        k: (
+            bids.layout.Query.NONE
+            if v is None
+            else (bids.layout.Query.ANY if v == "*" else v)
+        )
         for k, v in dct.items()
     }
 
diff --git a/giga_connectome/workflow.py b/giga_connectome/workflow.py
index 5fbada5..034e910 100644
--- a/giga_connectome/workflow.py
+++ b/giga_connectome/workflow.py
@@ -1,6 +1,7 @@
 """
 Process fMRIPrep outputs to timeseries based on denoising strategy.
 """
+
 from __future__ import annotations
 
 from giga_connectome import (
diff --git a/tools/download_templates.py b/tools/download_templates.py
index d79a421..20ee80a 100644
--- a/tools/download_templates.py
+++ b/tools/download_templates.py
@@ -2,6 +2,7 @@
 Set up templateflow with customised altases.
 Download atlases that are relevant.
 """
+
 from pathlib import Path
 
 from giga_connectome.logger import gc_logger
diff --git a/tools/mist2templateflow b/tools/mist2templateflow
index 4e0a2a3..e9c6b20 160000
--- a/tools/mist2templateflow
+++ b/tools/mist2templateflow
@@ -1 +1 @@
-Subproject commit 4e0a2a3688f344d197e6e753ca4c9bdc9b8ed5a4
+Subproject commit e9c6b2087ce698c873fea21433f1c7ed1fe762f0