Raise error if two-echo data are provided

.github/workflows/docker.yml

@@ -18,23 +18,6 @@ env:
   FORCE_COLOR: true
 
 jobs:
-  check-pixi:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v5
-        with:
-          fetch-depth: 200
-          fetch-tags: true
-          ref: ${{ github.ref }}
-      - uses: prefix-dev/[email protected]
-        with:
-          pixi-version: v0.55.0
-          run-install: false
-      - run: pixi lock --check
-
   build-container:
     runs-on: ubuntu-latest
     permissions:

.github/workflows/pixi-lock.yml

@@ -0,0 +1,55 @@
+on:
+  pull_request_target
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-lockfile:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout pull request
+        uses: actions/checkout@v5
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          fetch-depth: 0
+      - name: Find submitting repository
+        id: get-source-repo
+        uses: actions/github-script@v8
+        env:
+          OWNER: ${{ github.repository_owner }}
+          REPO: ${{ github.repository }}
+          PULL: ${{ github.event.number }}
+        with:
+          script: |
+            const { data } = await github.rest.pulls.get({
+              owner: process.env.OWNER,
+              repo: process.env.REPO.split('/')[1],
+              pull_number: process.env.PULL,
+            });
+            core.setOutput('remote', data.head.repo.html_url)
+            core.setOutput('branch', data.head.ref)
+      - name: Set git identity
+        run: |
+          git config --global user.name "nipreps[bot]"
+          git config --global user.email "[email protected]"
+      - uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.58.0
+          run-install: false
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
+      - name: Update lockfile
+        run: >
+          uvx datalad run -i pixi.lock -i pyproject.toml -o pixi.lock --
+          bash -c '! pixi lock --check || git checkout .'
+      - name: Push updated lockfile, if needed
+        run: |
+          git push $REMOTE HEAD:$BRANCH
+        env:
+          REMOTE: ${{ steps.get-source-repo.outputs.remote }}
+          BRANCH: ${{ steps.get-source-repo.outputs.branch }}

.github/workflows/test.yml

@@ -58,7 +58,7 @@ jobs:
           sudo apt update
           sudo apt install -y --no-install-recommends graphviz
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
         with:
@@ -72,6 +72,9 @@ jobs:
         run: tox c
       - name: Run tox
         run: tox -v --exit-and-dump-after 1200
+      - name: Minimize uv cache
+        run: uv cache prune --ci
+        if: ${{ always() }}
       - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -89,10 +92,13 @@ jobs:
         with:
           persist-credentials: false
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Install tox
         run: uv tool install tox --with=tox-uv
       - name: Show tox config
         run: tox c -e ${{ matrix.check }}
       - name: Run check
         run: tox -e ${{ matrix.check }}
+      - name: Minimize uv cache
+        run: uv cache prune --ci
+        if: ${{ always() }}

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.1
+    rev: v0.13.3
     hooks:
       - id: ruff-check
         args: [ --fix ]

fmriprep/interfaces/multiecho.py

@@ -68,6 +68,11 @@ class T2SMapInputSpec(CommandLineInputSpec):
             'monoexponential model is fit to the raw data.'
         ),
     )
+    n_exclude = traits.Int(
+        argstr='--exclude 0:%d',
+        position=5,
+        desc='Number of volumes from the beginning of the run to exclude from T2*/S0 estimation.',
+    )
 
 
 class T2SMapOutputSpec(TraitedSpec):

fmriprep/interfaces/patches.py

@@ -33,7 +33,7 @@
 import nipype.interfaces.io as nio
 from nipype.algorithms import confounds as nac
 from nipype.interfaces.base import File, traits
-from numpy.linalg.linalg import LinAlgError
+from numpy.linalg import LinAlgError
 
 
 class RobustACompCor(nac.ACompCor):

fmriprep/workflows/base.py

@@ -834,6 +834,16 @@ def init_single_subject_wf(
         fieldmap_id = estimator_map.get(bold_file)
         jacobian = False
 
+        if len(bold_series) == 2:
+            # This should only be reached if two-echo data are provided and echo-idx is not.
+            # Raise an error in this case, until we figure out how to support two-echo data.
+            bold_series_str = '\n\t'.join(bold_series)
+            raise RuntimeError(
+                'This BOLD series contains two echoes, which fMRIPrep does not support:\n'
+                f'\t{bold_series_str}\n'
+                'Please set "--echo-idx" to process one echo at a time.'
+            )
+
         if fieldmap_id:
             if 'fmap-jacobian' in config.workflow.force:
                 jacobian = True

fmriprep/workflows/bold/fit.py

@@ -981,7 +981,10 @@ def init_bold_native_wf(
         # Do NOT set motion_xfm on outputnode
         # This prevents downstream resamplers from double-dipping
         workflow.connect([
-            (inputnode, bold_t2s_wf, [('bold_mask', 'inputnode.bold_mask')]),
+            (inputnode, bold_t2s_wf, [
+                ('bold_mask', 'inputnode.bold_mask'),
+                ('dummy_scans', 'inputnode.skip_vols'),
+            ]),
             (boldref_bold, join_echos, [('out_file', 'bold_files')]),
             (join_echos, bold_t2s_wf, [('bold_files', 'inputnode.bold_file')]),
             (join_echos, outputnode, [('bold_files', 'bold_echos')]),

fmriprep/workflows/bold/t2s.py

@@ -107,7 +107,10 @@ def init_bold_t2s_wf(
 The optimally combined time series was carried forward as the *preprocessed BOLD*.
 """
 
-    inputnode = pe.Node(niu.IdentityInterface(fields=['bold_file', 'bold_mask']), name='inputnode')
+    inputnode = pe.Node(
+        niu.IdentityInterface(fields=['bold_file', 'bold_mask', 'skip_vols']),
+        name='inputnode',
+    )
 
     outputnode = pe.Node(niu.IdentityInterface(fields=['bold', 't2star_map']), name='outputnode')
 
@@ -122,7 +125,10 @@ def init_bold_t2s_wf(
     )
     workflow.connect([
         (inputnode, dilate_mask, [('bold_mask', 'in_mask')]),
-        (inputnode, t2smap_node, [('bold_file', 'in_files')]),
+        (inputnode, t2smap_node, [
+            ('bold_file', 'in_files'),
+            ('skip_vols', 'n_exclude'),
+        ]),
         (dilate_mask, t2smap_node, [('out_mask', 'mask_file')]),
         (t2smap_node, outputnode, [('optimal_comb', 'bold'),
                                    ('t2star_map', 't2star_map')]),

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "requests >= 2.27",
     "sdcflows >= 2.15.0",
     "smriprep >= 0.19.2",
-    "tedana >= 25.0.0",
+    "tedana >= 25.1.0",
     "templateflow >= 24.2.2",
     "transforms3d >= 0.4.2",
     "toml >= 0.10",