Merge pull request #761 from effigies/misc

[RTM] Remove skull_strip_ants option, fix docstring

docs/workflows.rst

@@ -26,7 +26,6 @@ slice-timing information and no fieldmap acquisitions):
                                 reportlets_dir='.',
                                 output_dir='.',
                                 bids_dir='.',
-                                skull_strip_ants=True,
                                 skull_strip_template='OASIS',
                                 template='MNI152NLin2009cAsym',
                                 output_spaces=['T1w', 'fsnative',
@@ -63,7 +62,6 @@ T1w/T2w preprocessing
                               template='MNI152NLin2009cAsym',
                               output_spaces=['T1w', 'fsnative',
                                              'template', 'fsaverage5'],
-                              skull_strip_ants=True,
                               skull_strip_template='OASIS',
                               freesurfer=True,
                               longitudinal=False,

fmriprep/cli/run.py

@@ -141,11 +141,6 @@ def get_parser():
                          help='add ICA_AROMA to your preprocessing stream')
     #  ANTs options
     g_ants = parser.add_argument_group('Specific options for ANTs registrations')
-    # g_ants.add_argument('--skull-strip-ants', dest="skull_strip_ants", action='store_true',
-    #                     help='use ANTs-based skull-stripping (default, slow))')
-    # g_ants.add_argument('--no-skull-strip-ants', dest="skull_strip_ants", action='store_false',
-    #                     help="don't use ANTs-based skull-stripping (use  AFNI instead, fast)")
-    # g_ants.set_defaults(skull_strip_ants=True)
     g_ants.add_argument('--skull-strip-template', action='store', default='OASIS',
                         choices=['OASIS', 'NKI'],
                         help='select ANTs skull-stripping template (default: OASIS))')
@@ -305,7 +300,6 @@ def create_workflow(opts):
         anat_only=opts.anat_only,
         longitudinal=opts.longitudinal,
         omp_nthreads=omp_nthreads,
-        skull_strip_ants=True,
         skull_strip_template=opts.skull_strip_template,
         work_dir=work_dir,
         output_dir=output_dir,

fmriprep/interfaces/freesurfer.py

@@ -67,8 +67,14 @@ class MakeMidthicknessInputSpec(fs.utils.MRIsExpandInputSpec):
 
 
 class MakeMidthickness(fs.MRIsExpand):
-    """ Variation on RobustTemplate that simply copies the source if a single
-    volume is provided. """
+    """ Variation on MRIsExpand that checks for an existing midthickness/graymid
+    surface, and copies if available.
+
+    mris_expand is an expensive operation, so this avoids re-running it when the
+    working directory is lost.
+    If users provide their own midthickness/graymid file, we assume they have
+    created it correctly.
+    """
     input_spec = MakeMidthicknessInputSpec
 
     @property

fmriprep/workflows/anatomical.py

@@ -32,7 +32,6 @@
 from niworkflows.nipype.pipeline import engine as pe
 
 from niworkflows.interfaces.registration import RobustMNINormalizationRPT
-from niworkflows.anat.skullstrip import afni_wf as init_skullstrip_afni_wf
 import niworkflows.data as nid
 from niworkflows.interfaces.masks import BrainExtractionRPT
 from niworkflows.interfaces.segmentation import FASTRPT, ReconAllRPT
@@ -46,7 +45,7 @@
 
 
 #  pylint: disable=R0914
-def init_anat_preproc_wf(skull_strip_ants, skull_strip_template, output_spaces, template, debug,
+def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
                          freesurfer, longitudinal, omp_nthreads, hires, reportlets_dir, output_dir,
                          name='anat_preproc_wf'):
     r"""
@@ -71,7 +70,6 @@ def init_anat_preproc_wf(skull_strip_ants, skull_strip_template, output_spaces,
                                   template='MNI152NLin2009cAsym',
                                   output_spaces=['T1w', 'fsnative',
                                                  'template', 'fsaverage5'],
-                                  skull_strip_ants=True,
                                   skull_strip_template='OASIS',
                                   freesurfer=True,
                                   longitudinal=False,
@@ -80,9 +78,6 @@ def init_anat_preproc_wf(skull_strip_ants, skull_strip_template, output_spaces,
 
     **Parameters**
 
-        skull_strip_ants : bool
-            Use ANTs BrainExtraction.sh-based skull-stripping workflow.
-            If ``False``, uses a faster AFNI-based workflow
         skull_strip_template : str
             Name of ANTs skull-stripping template ('OASIS' or 'NKI')
         output_spaces : list
@@ -201,13 +196,10 @@ def init_anat_preproc_wf(skull_strip_ants, skull_strip_template, output_spaces,
     # Bias field correction is handled in skull strip workflows.
 
     # 3. Skull-stripping
-    if skull_strip_ants:
-        skullstrip_wf = init_skullstrip_ants_wf(name='skullstrip_ants_wf',
-                                                skull_strip_template=skull_strip_template,
-                                                debug=debug,
-                                                omp_nthreads=omp_nthreads)
-    else:
-        skullstrip_wf = init_skullstrip_afni_wf(name='skullstrip_afni_wf')
+    skullstrip_ants_wf = init_skullstrip_ants_wf(name='skullstrip_ants_wf',
+                                                 skull_strip_template=skull_strip_template,
+                                                 debug=debug,
+                                                 omp_nthreads=omp_nthreads)
 
     # 4. Segmentation
     t1_seg = pe.Node(FASTRPT(generate_report=True, segments=True,
@@ -267,11 +259,11 @@ def len_above_thresh(in_list, threshold, longitudinal):
             (('out_file', len_above_thresh, 2, longitudinal), 'no_iteration'),
             (('out_file', add_suffix, '_template'), 'out_file')]),
         (t1_merge, t1_reorient, [('out_file', 'in_file')]),
-        (t1_reorient, skullstrip_wf, [('out_file', 'inputnode.in_file')]),
-        (skullstrip_wf, t1_seg, [('outputnode.out_file', 'in_files')]),
-        (skullstrip_wf, outputnode, [('outputnode.bias_corrected', 't1_preproc'),
-                                     ('outputnode.out_file', 't1_brain'),
-                                     ('outputnode.out_mask', 't1_mask')]),
+        (t1_reorient, skullstrip_ants_wf, [('out_file', 'inputnode.in_file')]),
+        (skullstrip_ants_wf, t1_seg, [('outputnode.out_file', 'in_files')]),
+        (skullstrip_ants_wf, outputnode, [('outputnode.bias_corrected', 't1_preproc'),
+                                          ('outputnode.out_file', 't1_brain'),
+                                          ('outputnode.out_mask', 't1_mask')]),
         (t1_seg, outputnode, [('tissue_class_map', 't1_seg'),
                               ('probability_maps', 't1_tpms')]),
     ])
@@ -286,9 +278,9 @@ def len_above_thresh(in_list, threshold, longitudinal):
         mni_tpms.inputs.reference_image = ref_img
 
         workflow.connect([
-            (skullstrip_wf, t1_2_mni, [('outputnode.bias_corrected', 'moving_image')]),
-            (skullstrip_wf, t1_2_mni, [('outputnode.out_mask', 'moving_mask')]),
-            (skullstrip_wf, mni_mask, [('outputnode.out_mask', 'input_image')]),
+            (skullstrip_ants_wf, t1_2_mni, [('outputnode.bias_corrected', 'moving_image')]),
+            (skullstrip_ants_wf, t1_2_mni, [('outputnode.out_mask', 'moving_mask')]),
+            (skullstrip_ants_wf, mni_mask, [('outputnode.out_mask', 'input_image')]),
             (t1_2_mni, mni_mask, [('composite_transform', 'transforms')]),
             (t1_seg, mni_seg, [('tissue_class_map', 'input_image')]),
             (t1_2_mni, mni_seg, [('composite_transform', 'transforms')]),
@@ -314,7 +306,7 @@ def len_above_thresh(in_list, threshold, longitudinal):
                 ('subjects_dir', 'inputnode.subjects_dir'),
                 ('subject_id', 'inputnode.subject_id')]),
             (t1_reorient, surface_recon_wf, [('out_file', 'inputnode.t1w')]),
-            (skullstrip_wf, surface_recon_wf, [
+            (skullstrip_ants_wf, surface_recon_wf, [
                 ('outputnode.out_file', 'inputnode.skullstripped_t1')]),
             (surface_recon_wf, outputnode, [
                 ('outputnode.subjects_dir', 'subjects_dir'),
@@ -324,21 +316,18 @@ def len_above_thresh(in_list, threshold, longitudinal):
         ])
 
     anat_reports_wf = init_anat_reports_wf(
-        reportlets_dir=reportlets_dir, skull_strip_ants=skull_strip_ants,
-        output_spaces=output_spaces, template=template, freesurfer=freesurfer)
+        reportlets_dir=reportlets_dir, output_spaces=output_spaces, template=template,
+        freesurfer=freesurfer)
     workflow.connect([
         (inputnode, anat_reports_wf, [
             (('t1w', fix_multi_T1w_source_name), 'inputnode.source_file')]),
         (t1_template_dimensions, anat_reports_wf, [
             ('out_report', 'inputnode.t1_conform_report')]),
+        (skullstrip_ants_wf, anat_reports_wf, [
+            ('outputnode.out_report', 'inputnode.t1_skull_strip_report')]),
         (t1_seg, anat_reports_wf, [('out_report', 'inputnode.t1_seg_report')]),
     ])
 
-    if skull_strip_ants:
-        workflow.connect([
-            (skullstrip_wf, anat_reports_wf, [
-                ('outputnode.out_report', 'inputnode.t1_skull_strip_report')])
-        ])
     if freesurfer:
         workflow.connect([
             (surface_recon_wf, anat_reports_wf, [
@@ -804,7 +793,7 @@ def init_gifti_surface_wf(name='gifti_surface_wf'):
     return workflow
 
 
-def init_anat_reports_wf(reportlets_dir, skull_strip_ants, output_spaces,
+def init_anat_reports_wf(reportlets_dir, output_spaces,
                          template, freesurfer, name='anat_reports_wf'):
     """
     Set up a battery of datasinks to store reports in the right location
@@ -840,15 +829,12 @@ def init_anat_reports_wf(reportlets_dir, skull_strip_ants, output_spaces,
     workflow.connect([
         (inputnode, ds_t1_conform_report, [('source_file', 'source_file'),
                                            ('t1_conform_report', 'in_file')]),
+        (inputnode, ds_t1_skull_strip_report, [('source_file', 'source_file'),
+                                               ('t1_skull_strip_report', 'in_file')]),
         (inputnode, ds_t1_seg_report, [('source_file', 'source_file'),
                                        ('t1_seg_report', 'in_file')]),
     ])
 
-    if skull_strip_ants:
-        workflow.connect([
-            (inputnode, ds_t1_skull_strip_report, [('source_file', 'source_file'),
-                                                   ('t1_skull_strip_report', 'in_file')])
-        ])
     if freesurfer:
         workflow.connect([
             (inputnode, ds_recon_report, [('source_file', 'source_file'),

fmriprep/workflows/base.py

@@ -32,7 +32,7 @@
 
 def init_fmriprep_wf(subject_list, task_id, run_uuid,
                      ignore, debug, low_mem, anat_only, longitudinal, omp_nthreads,
-                     skull_strip_ants, skull_strip_template, work_dir, output_dir, bids_dir,
+                     skull_strip_template, work_dir, output_dir, bids_dir,
                      freesurfer, output_spaces, template, medial_surface_nan, hires,
                      use_bbr, bold2t1w_dof, fmap_bspline, fmap_demean, use_syn, force_syn,
                      use_aroma, ignore_aroma_err, output_grid_ref):
@@ -57,7 +57,6 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,
                               anat_only=False,
                               longitudinal=False,
                               omp_nthreads=1,
-                              skull_strip_ants=True,
                               skull_strip_template='OASIS',
                               work_dir='.',
                               output_dir='.',
@@ -100,9 +99,6 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,
             See sub-workflows for specific differences
         omp_nthreads : int
             Maximum number of threads an individual process may use
-        skull_strip_ants : bool
-            Use ANTs BrainExtraction.sh-based skull-stripping workflow
-            If ``False``, uses a faster AFNI-based workflow
         skull_strip_template : str
             Name of ANTs skull-stripping template ('OASIS' or 'NKI')
         work_dir : str
@@ -173,7 +169,6 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,
                                                    anat_only=anat_only,
                                                    longitudinal=longitudinal,
                                                    omp_nthreads=omp_nthreads,
-                                                   skull_strip_ants=skull_strip_ants,
                                                    skull_strip_template=skull_strip_template,
                                                    reportlets_dir=reportlets_dir,
                                                    output_dir=output_dir,
@@ -209,7 +204,7 @@ def init_fmriprep_wf(subject_list, task_id, run_uuid,
 
 def init_single_subject_wf(subject_id, task_id, name,
                            ignore, debug, low_mem, anat_only, longitudinal, omp_nthreads,
-                           skull_strip_ants, skull_strip_template, reportlets_dir, output_dir,
+                           skull_strip_template, reportlets_dir, output_dir,
                            bids_dir, freesurfer, output_spaces, template, medial_surface_nan,
                            hires, use_bbr, bold2t1w_dof, fmap_bspline, fmap_demean, use_syn,
                            force_syn, output_grid_ref, use_aroma, ignore_aroma_err):
@@ -237,7 +232,6 @@ def init_single_subject_wf(subject_id, task_id, name,
                                     reportlets_dir='.',
                                     output_dir='.',
                                     bids_dir='.',
-                                    skull_strip_ants=True,
                                     skull_strip_template='OASIS',
                                     template='MNI152NLin2009cAsym',
                                     output_spaces=['T1w', 'fsnative',
@@ -279,9 +273,6 @@ def init_single_subject_wf(subject_id, task_id, name,
             See sub-workflows for specific differences
         omp_nthreads : int
             Maximum number of threads an individual process may use
-        skull_strip_ants : bool
-            Use ANTs BrainExtraction.sh-based skull-stripping workflow
-            If ``False``, uses a faster AFNI-based workflow
         skull_strip_template : str
             Name of ANTs skull-stripping template ('OASIS' or 'NKI')
         reportlets_dir : str
@@ -384,7 +375,6 @@ def init_single_subject_wf(subject_id, task_id, name,
 
     # Preprocessing of T1w (includes registration to MNI)
     anat_preproc_wf = init_anat_preproc_wf(name="anat_preproc_wf",
-                                           skull_strip_ants=skull_strip_ants,
                                            skull_strip_template=skull_strip_template,
                                            output_spaces=output_spaces,
                                            template=template,

fmriprep/workflows/tests/test_base.py

@@ -20,7 +20,6 @@ def test_single_subject_wf(self, _):
                                          anat_only=False,
                                          longitudinal=False,
                                          omp_nthreads=1,
-                                         skull_strip_ants=False,
                                          skull_strip_template='OASIS',
                                          reportlets_dir='.',
                                          output_dir='.',