fix: apply recenter only within the mask

FSL PRELUDE will return some values unwrapped below zero, making it hard
to differenciate these pixels from the mask.
This commit addresses that particular issue.

Author: oesteban

sdcflows/workflows/phdiff.py

@@ -141,6 +141,7 @@ def init_phdiff_wf(omp_nthreads, name='phdiff_wf'):
         (inputnode, phmap2rads, [('phasediff', 'in_file')]),
         (phmap2rads, prelude, [('out_file', 'phase_file')]),
         (prelude, recenter, [('unwrapped_phase_file', 'in_file')]),
+        (bet, recenter, [('mask_file', 'in_mask')]),
         (recenter, denoise, [('out', 'in_file')]),
         (denoise, demean, [('out_file', 'in_file')]),
         (demean, cleanup_wf, [('out', 'inputnode.in_file')]),
@@ -154,9 +155,9 @@ def init_phdiff_wf(omp_nthreads, name='phdiff_wf'):
     return workflow
 
 
-def _recenter(in_file, offset=None):
+def _recenter(in_file, in_mask=None, offset=None):
     """Recenter the phase-map distribution to the -pi..pi range."""
-    from os.path import basename
+    from os import getcwd
     import numpy as np
     import nibabel as nb
     from nipype.utils.filemanip import fname_presuffix
@@ -165,8 +166,15 @@ def _recenter(in_file, offset=None):
         offset = np.pi
 
     nii = nb.load(in_file)
-    data = nii.get_fdata(dtype='float32') - offset
+    data = nii.get_fdata(dtype='float32')
 
-    out_file = fname_presuffix(basename(in_file), suffix='_recentered')
+    msk = data > 1.e-6
+    if in_mask is not None:
+        msk = nb.load(in_mask).get_fdata(dtype='float32') > 1.e-4
+
+    data[msk] -= offset
+
+    out_file = fname_presuffix(in_file, suffix='_recentered',
+                               newpath=getcwd())
     nb.Nifti1Image(data, nii.affine, nii.header).to_filename(out_file)
     return out_file