wip

sdcflows/workflows/fieldmap.py

@@ -0,0 +1,64 @@
+DEFAULT_MEMORY_MIN_GB = 0.01
+
+
+def init_fmap_preproc_wf(
+    *,
+    bids_root,
+    input_data,
+    output_dir,
+    debug=False,
+    omp_nthreads=None,
+    name='fmap_preproc_wf',
+):
+    """
+    Stage the fieldmap preprocessing steps of *SDCFlows*.
+
+    This workflow takes at the input a set of images from which the fieldmap
+    could be theoretically estimated by one of the available implementations.
+    The workflow API is thought out to be consistent with that of
+    :py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf` in the sense that
+    it takes some specific inputs and generates some expected derivatives.
+
+    The particular estimation strategy is inferred from the actual inputs
+    given by ``input_data``.
+
+    Workflow Graph
+        .. workflow::
+            :graph2use: orig
+            :simple_form: yes
+            from sdcflows.workflows.fieldmap import init_fmap_preproc_wf
+            wf = init_fmap_preproc_wf(
+                bids_root='.',
+                input_data=[
+                    {
+                        "filename": "/data/sub-01/fmap/sub-01_epi.nii.gz",
+                        "PhaseEncodingDirection": "j",
+                        "TotalReadoutTime": "0.065",
+                        "IntendedFor": "func/sub-01_task-rest_bold.nii.gz"
+                    },
+                    {
+                        "filename": "/data/sub-01/func/sub-01_task-rest_sbref.nii.gz",
+                        "PhaseEncodingDirection": "j-",
+                        "TotalReadoutTime": "0.065"
+                    }
+                ],
+                output_dir="/data/derivatives/sdcflows-1.3.1",
+            )
+
+    Parameters
+    ----------
+    bids_root : :obj:`str`
+        Path of the input BIDS dataset root
+    output_dir : :obj:`str`
+        Directory in which to save derivatives
+    input_data : :obj:`list` of :obj:`dict`
+        The input data that can be used to estimate a fieldmap.
+    debug : :obj:`bool`
+        Enable debugging outputs
+    omp_nthreads : :obj:`int`
+        Maximum number of threads an individual process may use
+    name : :obj:`str`, optional
+        Workflow name (default: anat_preproc_wf)
+
+    """
+    return None