fixing problems with templates and segmentations

Author: oesteban

Dockerfile

@@ -161,10 +161,13 @@ RUN pip install "datalad==0.10.0" && \
     rm -rf ~/.cache/pip
 
 RUN git config --global user.name "First Last" && \
-    git config --global user.email "[email protected]" && \
-    datalad install -r https://github.com/templateflow/templateflow.git
-RUN datalad get $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/*_T1w.nii.gz \
+    git config --global user.email "[email protected]"
+
+RUN datalad install -r https://github.com/templateflow/templateflow.git && \
+    datalad get $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/*_T1w.nii.gz \
                 $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/*_desc-brain_mask.nii.gz \
+                $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz \
+                $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-DKT31_dseg.nii.gz \
                 $TEMPLATEFLOW_HOME/tpl-MNI152Lin/*_T1w.nii.gz \
                 $TEMPLATEFLOW_HOME/tpl-MNI152Lin/*_desc-brain_mask.nii.gz \
                 $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs/*_T1w.nii.gz \

fmriprep/workflows/bold/util.py

@@ -275,7 +275,7 @@ def init_enhance_and_skullstrip_bold_wf(
     apply_mask = pe.Node(fsl.ApplyMask(), name='apply_mask')
 
     if not pre_mask:
-        bold_template = get_template('fMRIPrep', 'space-MNI_res-02_boldref.nii.gz')
+        bold_template = get_template('MNI152NLin2009cAsym', 'res-02_desc-fMRIPrep_boldref.nii.gz')
         brain_mask = get_template('MNI152NLin2009cAsym', 'res-02_desc-brain_mask.nii.gz')
 
         # Initialize transforms with antsAI