Merge pull request #374 from nipreps/fix/relative-paths-phasediff-wf

oesteban · web-flow · commit e40b2f12a701 · 2023-07-07T14:13:20.000+02:00
FIX: Nipype workflows like to be passed absolute paths (phasediff fieldmap)
diff --git a/sdcflows/fieldmaps.py b/sdcflows/fieldmaps.py
@@ -450,10 +450,10 @@ def get_workflow(self, **kwargs):
             kwargs["mode"] = str(self.method).rpartition(".")[-1].lower()
             self._wf = init_fmap_wf(**kwargs)
             self._wf.inputs.inputnode.magnitude = [
-                str(f.path) for f in self.sources if f.suffix.startswith("magnitude")
+                str(f.path.absolute()) for f in self.sources if f.suffix.startswith("magnitude")
             ]
             self._wf.inputs.inputnode.fieldmap = [
-                (str(f.path), f.metadata)
+                (str(f.path.absolute()), f.metadata)
                 for f in self.sources
                 if f.suffix in ("fieldmap", "phasediff", "phase2", "phase1")
             ]

Original file line number	Diff line number	Diff line change
`@@ -450,10 +450,10 @@ def get_workflow(self, **kwargs):`
`450`	`450`	`kwargs["mode"] = str(self.method).rpartition(".")[-1].lower()`
`451`	`451`	`self._wf = init_fmap_wf(**kwargs)`
`452`	`452`	`self._wf.inputs.inputnode.magnitude = [`
`453`		`- str(f.path) for f in self.sources if f.suffix.startswith("magnitude")`
	`453`	`+ str(f.path.absolute()) for f in self.sources if f.suffix.startswith("magnitude")`
`454`	`454`	`]`
`455`	`455`	`self._wf.inputs.inputnode.fieldmap = [`
`456`		`- (str(f.path), f.metadata)`
	`456`	`+ (str(f.path.absolute()), f.metadata)`
`457`	`457`	`for f in self.sources`
`458`	`458`	`if f.suffix in ("fieldmap", "phasediff", "phase2", "phase1")`
`459`	`459`	`]`