fix: consider blip up or down of phase encoding

Author: oesteban

sdcflows/workflows/fit/syn.py

@@ -293,7 +293,7 @@ def _extract_field(in_file, epi_meta):
     >>> nii.shape
     (10, 10, 10)
 
-    >>> np.allclose(nii.get_fdata(), 200)
+    >>> np.allclose(nii.get_fdata(), -200)
     True
 
     """
@@ -308,7 +308,7 @@ def _extract_field(in_file, epi_meta):
         np.squeeze(fieldnii.get_fdata(dtype="float32"))[
             ..., "ijk".index(epi_meta[1]["PhaseEncodingDirection"][0])
         ]
-        / trt
+        / trt * (-1.0 if epi_meta[1]["PhaseEncodingDirection"].endswith("-") else 1.0)
     )
     out_file = fname_presuffix(in_file[0], suffix="_fieldmap")
     nii = nb.Nifti1Image(data, fieldnii.affine, None)

sdcflows/workflows/fit/tests/test_syn.py

@@ -23,7 +23,7 @@ def test_syn_wf(tmpdir, datadir, workdir, outdir):
             / "sdcflows-tests"
             / "sub-100185_task-machinegame_run-1_boldref.nii.gz"
         ),
-        {"PhaseEncodingDirection": "j", "TotalReadoutTime": 0.005},
+        {"PhaseEncodingDirection": "j-", "TotalReadoutTime": 0.005},
     )
     syn_wf.inputs.inputnode.epi_mask = str(
         derivs_path
@@ -74,7 +74,7 @@ def test_syn_wf(tmpdir, datadir, workdir, outdir):
 
         fmap_reports_wf = init_fmap_reports_wf(
             output_dir=str(outdir),
-            fmap_type="pepolar",
+            fmap_type="sdcsyn",
         )
         fmap_reports_wf.inputs.inputnode.source_files = [
             str(