Merge pull request #1106 from effigies/enh/ccfm_rf

[ENH] Add constrained cost-function masking to T1-MNI registration

Author: effigies

docs/environment.yml

@@ -28,4 +28,4 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows>=0.3.11
+    - git+https://github.com/poldracklab/niworkflows.git@e2b93ecdc7b6e52ee02466bf5d3be5bdb6d33beb#egg=niworkflows-0.3.12-dev

fmriprep/info.py

@@ -80,6 +80,8 @@
 ]
 
 LINKS_REQUIRES = [
+    'git+https://github.com/poldracklab/niworkflows.git@'
+    'e2b93ecdc7b6e52ee02466bf5d3be5bdb6d33beb#egg=niworkflows-0.3.12-dev',
 ]
 
 TESTS_REQUIRES = [

fmriprep/interfaces/bids.py

@@ -105,6 +105,7 @@ class BIDSDataGrabberOutputSpec(TraitedSpec):
     bold = OutputMultiPath(desc='output functional images')
     sbref = OutputMultiPath(desc='output sbrefs')
     t1w = OutputMultiPath(desc='output T1w images')
+    roi = OutputMultiPath(desc='output ROI images')
     t2w = OutputMultiPath(desc='output T2w images')
     flair = OutputMultiPath(desc='output FLAIR images')
 
@@ -148,7 +149,7 @@ def _run_interface(self, runtime):
             raise FileNotFoundError('No functional images found for subject sub-{}'.format(
                 self.inputs.subject_id))
 
-        for imtype in ['bold', 't2w', 'flair', 'fmap', 'sbref']:
+        for imtype in ['bold', 't2w', 'flair', 'fmap', 'sbref', 'roi']:
             if not bids_dict[imtype]:
                 LOGGER.warn('No \'{}\' images found for sub-{}'.format(
                     imtype, self.inputs.subject_id))

fmriprep/utils/bids.py

@@ -165,6 +165,8 @@ def collect_data(dataset, participant_label, task=None):
                 'extensions': ['nii', 'nii.gz']},
         't1w': {'subject': participant_label, 'type': 'T1w',
                 'extensions': ['nii', 'nii.gz']},
+        'roi': {'subject': participant_label, 'type': 'roi',
+                'extensions': ['nii', 'nii.gz']},
     }
 
     if task:

fmriprep/workflows/anatomical.py

@@ -177,7 +177,7 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=['t1w', 't2w', 'flair', 'subjects_dir', 'subject_id']),
+        niu.IdentityInterface(fields=['t1w', 't2w', 'roi', 'flair', 'subjects_dir', 'subject_id']),
         name='inputnode')
     outputnode = pe.Node(niu.IdentityInterface(
         fields=['t1_preproc', 't1_brain', 't1_mask', 't1_seg', 't1_tpms',
@@ -302,6 +302,7 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
         mni_tpms.inputs.reference_image = ref_img
 
         workflow.connect([
+            (inputnode, t1_2_mni, [('roi', 'lesion_mask')]),
             (skullstrip_ants_wf, t1_2_mni, [('outputnode.bias_corrected', 'moving_image')]),
             (buffernode, t1_2_mni, [('t1_mask', 'moving_mask')]),
             (buffernode, mni_mask, [('t1_mask', 'input_image')]),

fmriprep/workflows/base.py

@@ -419,6 +419,7 @@ def init_single_subject_wf(subject_id, task_id, name,
         (bids_info, summary, [('subject_id', 'subject_id')]),
         (bidssrc, anat_preproc_wf, [('t1w', 'inputnode.t1w'),
                                     ('t2w', 'inputnode.t2w'),
+                                    ('roi', 'inputnode.roi'),
                                     ('flair', 'inputnode.flair')]),
         (summary, anat_preproc_wf, [('subject_id', 'inputnode.subject_id')]),
         (bidssrc, ds_summary_report, [(('t1w', fix_multi_T1w_source_name), 'source_file')]),

requirements.txt

@@ -1,2 +1,2 @@
-niworkflows>=0.3.11
+git+https://github.com/poldracklab/niworkflows.git@e2b93ecdc7b6e52ee02466bf5d3be5bdb6d33beb#egg=niworkflows-0.3.12-dev
 versioneer