Work on unwrapping.

src/fmripost_phase/interfaces/misc.py

@@ -56,3 +56,34 @@ def _run_interface(self, runtime):
         self._results['out_file'] = os.path.abspath(os.path.join(runtime.cwd, 'cropped.nii.gz'))
         img.to_filename(self._results['out_file'])
         return runtime
+
+
+class _DictToJSONInputSpec(BaseInterfaceInputSpec):
+    in_dicts = traits.List(traits.Dict, desc='input dictionary')
+
+
+class _DictToJSONOutputSpec(TraitedSpec):
+    json_files = traits.List(File(exists=True), desc='output files')
+
+
+class DictToJSON(SimpleInterface):
+    """Remove non-steady-state volumes from a 4D NIfTI."""
+
+    input_spec = _DictToJSONInputSpec
+    output_spec = _DictToJSONOutputSpec
+
+    def _run_interface(self, runtime):
+        import json
+
+        json_files = []
+        for idx, in_dict in enumerate(self.inputs.in_dicts):
+            json_file = os.path.abspath(os.path.join(runtime.cwd, f'dict_{idx}.json'))
+
+            with open(json_file, 'w') as fobj:
+                json.dump(in_dict, fobj, indent=4, sort_keys=True)
+
+            json_files.append(json_file)
+
+        self._results['json_files'] = json_files
+
+        return runtime

src/fmripost_phase/interfaces/warpkit.py

@@ -33,14 +33,14 @@
 
 
 class _MEDICInputSpec(CommandLineInputSpec):
-    mag_files = traits.List(
+    magnitude = traits.List(
         File(exists=True),
         argstr='--magnitude %s',
         mandatory=True,
         minlen=2,
         desc='Magnitude image(s) to verify registration',
     )
-    phase_files = traits.List(
+    phase = traits.List(
         File(exists=True),
         argstr='--phase %s',
         mandatory=True,
@@ -124,19 +124,19 @@ def _list_outputs(self):
 
 
 class _WarpkitUnwrapInputSpec(CommandLineInputSpec):
-    mag_files = traits.List(
+    magnitude = traits.List(
         File(exists=True),
         argstr='--magnitude %s',
         mandatory=True,
         minlen=2,
         desc='Magnitude image(s) to verify registration',
     )
-    phase_files = traits.List(
+    phase = traits.List(
         File(exists=True),
         argstr='--phase %s',
         mandatory=True,
         minlen=2,
-        desc='Phase image(s) to verify registration',
+        desc='Phase image(s) to unwrap',
     )
     metadata = traits.List(
         File(exists=True),
@@ -146,7 +146,7 @@ class _WarpkitUnwrapInputSpec(CommandLineInputSpec):
         desc='Metadata corresponding to the inputs',
     )
     prefix = traits.Str(
-        'medic',
+        'warpkit',
         argstr='--out_prefix %s',
         usedefault=True,
         desc='Prefix for output files',
@@ -178,39 +178,27 @@ class _WarpkitUnwrapInputSpec(CommandLineInputSpec):
 
 
 class _WarpkitUnwrapOutputSpec(TraitedSpec):
-    native_field_map = File(
-        exists=True,
-        desc='4D native (distorted) space field map in Hertz',
-    )
-    displacement_map = File(
-        exists=True,
-        desc='4D displacement map in millimeters',
-    )
-    field_map = File(
-        exists=True,
-        desc='4D undistorted field map in Hertz',
+    unwrapped = traits.List(
+        File(exists=True),
+        desc='Unwrapped phase data',
     )
 
 
 class WarpkitUnwrap(CommandLine):
     """Unwrap multi-echo phase data with warpkit."""
 
-    _cmd = 'medic'
+    _cmd = 'warpkit_unwrap'
     input_spec = _WarpkitUnwrapInputSpec
     output_spec = _WarpkitUnwrapOutputSpec
 
     def _list_outputs(self):
         outputs = self._outputs().get()
         out_dir = os.getcwd()
-        outputs['native_field_map'] = os.path.join(
-            out_dir,
-            f'{self.inputs.prefix}_fieldmaps_native.nii',
-        )
-        outputs['displacement_map'] = os.path.join(
-            out_dir,
-            f'{self.inputs.prefix}_displacementmaps.nii',
-        )
-        outputs['field_map'] = os.path.join(out_dir, f'{self.inputs.prefix}_fieldmaps.nii')
+        out_prefix = os.path.join(out_dir, self.inputs.prefix)
+        outputs['unwrapped'] = [
+            f'{out_prefix}_echo-{i_echo + 1}_phase.nii.gz' for i_echo in
+            range(len(self.inputs.phase))
+        ]
         return outputs
 
 

src/fmripost_phase/workflows/base.py

@@ -286,7 +286,7 @@ def init_single_run_wf(bold_file):
     from fmripost_phase.interfaces.bids import DerivativesDataSink
     from fmripost_phase.interfaces.complex import Scale2Radians
     from fmripost_phase.interfaces.laynii import LayNiiPhaseJolt
-    from fmripost_phase.interfaces.misc import RemoveNSS
+    from fmripost_phase.interfaces.misc import DictToJSON, RemoveNSS
     from fmripost_phase.interfaces.warpkit import ROMEOUnwrap, WarpkitUnwrap
     from fmripost_phase.utils.bids import collect_derivatives, extract_entities
     from fmripost_phase.workflows.confounds import init_bold_confs_wf
@@ -519,11 +519,27 @@ def init_single_run_wf(bold_file):
         )
         workflow.connect([(remove_phase_nss, phase_to_radians2, [('out_file', 'in_file')])])
 
+        # Convert metadata dictionaries to JSON files
+        metadata_to_jsons = pe.Node(
+            DictToJSON(),
+            name='metadata_to_jsons',
+        )
+        workflow.connect([(inputnode, metadata_to_jsons, [('metadata', 'in_dicts')])])
+
         unwrap_phase = pe.Node(
-            WarpkitUnwrap(),
+            WarpkitUnwrap(
+                noise_frames=0,
+                debug=False,
+                wrap_limit=False,
+                n_cpus=config.nipype.omp_nthreads,
+            ),
             name='unwrap_phase',
+            n_procs=config.nipype.omp_nthreads,
         )
-        workflow.connect([(phase_to_radians2, unwrap_phase, [('out_file', 'phase')])])
+        workflow.connect([
+            (phase_to_radians2, unwrap_phase, [('out_file', 'phase')]),
+            (metadata_to_jsons, unwrap_phase, [('json_files', 'metadata')]),
+        ])  # fmt:skip
     else:
         # ROMEO uses data in radians (-pi to pi)
         unwrap_phase = pe.Node(
@@ -536,7 +552,9 @@ def init_single_run_wf(bold_file):
         )
         workflow.connect([(remove_phase_nss, unwrap_phase, [('out_file', 'phase')])])
 
-    workflow.connect([(remove_mag_nss, unwrap_phase, [('out_file', 'magnitude')])])
+    workflow.connect([
+        (remove_mag_nss, unwrap_phase, [('out_file', 'magnitude')]),
+    ])  # fmt:skip
 
     # Warp magnitude and phase data to BOLD reference space
     mag_boldref_wf = init_bold_volumetric_resample_wf(