🐛 Restore outputs removed from "freesurfer_abcd_preproc" to "freesurfer_reconall" (#2192)

Author: shnizzedy

.github/workflows/smoke_test_participant.yml

@@ -145,9 +145,10 @@ jobs:
           echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
           cat $GITHUB_ENV
       - name: setup-conda
-        uses: s-weigand/setup-[email protected]
+        uses: conda-incubator/setup-[email protected]
       - name: Set up datalad-OSF
         run: |
+          sudo apt-get update && sudo apt-get install -y git-annex
           git config --global user.email "[email protected]"
           git config --global user.name "Theodore (Machine User)"
           yes | conda install -c conda-forge datalad
@@ -203,15 +204,23 @@ jobs:
           echo DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}" | tr '[:upper:]' '[:lower:]'):$TAG >> $GITHUB_ENV
           cat $GITHUB_ENV
       - name: setup-conda
-        uses: s-weigand/[email protected]
+        uses: conda-incubator/[email protected]
+        with:
+          activate-environment: datalad-osf
+          channels: conda-forge
+          conda-remove-defaults: "true"
+          python-version: 3.12
       - name: Set up datalad-OSF
         run: |
+          sudo apt-get update && sudo apt-get install -y git-annex
           git config --global user.email "[email protected]"
           git config --global user.name "Theodore (Machine User)"
           yes | conda install -c conda-forge datalad
           pip install datalad-osf
       - name: Get rodent test data
         run: |
+          export GIT_TRACE=1
+          export DATALAD_LOG_LEVEL=DEBUG
           datalad clone osf://uya3r test-data
       - name: Run rodent smoke test
         run: |

CPAC/anat_preproc/anat_preproc.py

@@ -2904,6 +2904,18 @@ def freesurfer_abcd_preproc(wf, cfg, strat_pool, pipe_num, opt=None):
         "pipeline-fs_brainmask",
         "pipeline-fs_wmparc",
         "pipeline-fs_T1",
+        *[
+            f"pipeline-fs_hemi-{hemi}_{entity}"
+            for hemi in ["L", "R"]
+            for entity in [
+                "desc-surface_curv",
+                *[
+                    f"desc-surfaceMesh_{_}"
+                    for _ in ["pial", "smoothwm", "sphere", "white"]
+                ],
+                *[f"desc-surfaceMap_{_}" for _ in ["sulc", "thickness", "volume"]],
+            ]
+        ],
         *freesurfer_abcd_preproc.outputs,
         # we're grabbing the postproc outputs and appending them to
         # the reconall outputs