[ENH] Allow templates other than MNI152NLin2009cAsym

This is possible leveraging TemplateFlow. This PR closes nipreps#11, although
it does not implement the feature of allowing setting more than just one
spatial normalization target.

Modified ds054's build in CircleCI to test against ``MNI152Lin``.

.circleci/config.yml

@@ -418,7 +418,7 @@ jobs:
                 poldracklab/smriprep:latest \
                 /tmp/data/ds054 /tmp/ds054/derivatives participant \
                 -w /tmp/ds054/work --fs-no-reconall --sloppy --write-graph \
-                --mem-gb 4 --ncpus 2 --omp-nthreads 2 -vv \
+                --template MNI152Lin --mem-gb 4 --ncpus 2 --omp-nthreads 2 -vv \
                 --fs-license-file /tmp/fslicense/license.txt
       - save_cache:
          key: ds054-anat-v2-{{ .Branch }}-{{ epoch }}

requirements.txt

@@ -1,5 +1,5 @@
 templateflow>=0.0.3
-git+https://github.com/oesteban/niworkflows.git@c7432ec841706fbb4d9573567320529a09f4d156#niworkflows-0.5.3
+git+https://github.com/oesteban/niworkflows.git@236dc42b2f49054da88ed232b75e5cd5ff718426#niworkflows-0.5.3
 grabbit==0.2.3
 pybids==0.6.5
 indexed_gzip>=0.8.8

smriprep/__about__.py

@@ -62,7 +62,7 @@
 
 LINKS_REQUIRES = [
     'git+https://github.com/oesteban/niworkflows.git@'
-    'c7432ec841706fbb4d9573567320529a09f4d156#niworkflows-0.5.3',
+    '236dc42b2f49054da88ed232b75e5cd5ff718426#niworkflows-0.5.3',
 ]
 
 TESTS_REQUIRES = [

smriprep/interfaces/reports.py

@@ -14,15 +14,16 @@
 
 from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec,
-    File, Directory, InputMultiPath, Str, isdefined,
+    File, Directory, InputMultiObject, Str, isdefined,
     SimpleInterface)
 from nipype.interfaces import freesurfer as fs
 
 
 SUBJECT_TEMPLATE = """\t<ul class="elem-desc">
 \t\t<li>Subject ID: {subject_id}</li>
 \t\t<li>Structural images: {n_t1s:d} T1-weighted {t2w}</li>
-\t\t<li>Resampling targets: {fs_spaces}
+\t\t<li>Surface spaces: {fs_spaces}</li>
+{template}\
 \t\t<li>FreeSurfer reconstruction: {freesurfer_status}</li>
 \t</ul>
 """
@@ -52,12 +53,12 @@ def _run_interface(self, runtime):
 
 
 class SubjectSummaryInputSpec(BaseInterfaceInputSpec):
-    t1w = InputMultiPath(File(exists=True), desc='T1w structural images')
-    t2w = InputMultiPath(File(exists=True), desc='T2w structural images')
+    t1w = InputMultiObject(File(exists=True), desc='T1w structural images')
+    t2w = InputMultiObject(File(exists=True), desc='T2w structural images')
     subjects_dir = Directory(desc='FreeSurfer subjects directory')
     subject_id = Str(desc='Subject ID')
     fs_spaces = traits.List(desc='Target spaces')
-    template = traits.Enum('MNI152NLin2009cAsym', desc='Template space')
+    template = InputMultiObject(Str, desc='Template space')
 
 
 class SubjectSummaryOutputSpec(SummaryOutputSpec):
@@ -76,6 +77,11 @@ def _run_interface(self, runtime):
         return super(SubjectSummary, self)._run_interface(runtime)
 
     def _generate_segment(self):
+        if isdefined(self.inputs.template):
+            template = "\t\t<li>Volume standard spaces: {}</li>\n".format(
+                ', '.join(self.inputs.template) if isinstance(self.inputs.template, list)
+                else self.inputs.template)
+
         if not isdefined(self.inputs.subjects_dir):
             freesurfer_status = 'Not run'
         else:
@@ -95,6 +101,7 @@ def _generate_segment(self):
         return SUBJECT_TEMPLATE.format(subject_id=self.inputs.subject_id,
                                        n_t1s=len(self.inputs.t1w),
                                        t2w=t2w_seg,
+                                       template=template,
                                        fs_spaces=', '.join(self.inputs.fs_spaces),
                                        freesurfer_status=freesurfer_status)
 

smriprep/workflows/anatomical.py

@@ -316,6 +316,9 @@ def init_anat_preproc_wf(skull_strip_template, fs_spaces, template, debug,
     )
 
     # TODO isolate the spatial normalization workflow #############
+    if isinstance(template, list):
+        template = template[0]
+
     ref_img = get_template(template, 'res-01_T1w.nii.gz')
 
     t1_2_mni.inputs.template = template