[ENH] Expose bias-corrected T1w before skull-stripping
Addresses
@@ -150,11 +150,14 @@ def init_brain_extraction_wf(name='brain_extraction_wf',
**Outputs**
- bias_corrected
- The ``in_files`` input images, after :abbr:`INU (intensity non-uniformity)`
- correction.
+
+ out_file
+ Skull-stripped and :abbr:`INU (intensity non-uniformity)`-corrected ``in_files``
out_mask
Calculated brain mask
+ bias_corrected
+ The ``in_files`` input images, after :abbr:`INU (intensity non-uniformity)`
+ correction, before skull-stripping.
bias_image
The :abbr:`INU (intensity non-uniformity)` field estimated for each
input in ``in_files``
@@ -190,7 +193,7 @@ def init_brain_extraction_wf(name='brain_extraction_wf',
inputnode.inputs.in_mask = str(tpl_regmask_path)
outputnode = pe.Node(niu.IdentityInterface(
- fields=['bias_corrected', 'out_mask', 'bias_image', 'out_segm']),
+ fields=['out_file', 'out_mask', 'bias_corrected', 'bias_image', 'out_segm']),
name='outputnode')
trunc = pe.MapNode(ImageMath(operation='TruncateImageIntensity', op2='0.01 0.999 256'),
@@ -285,8 +288,9 @@ def init_brain_extraction_wf(name='brain_extraction_wf',
(inu_n4, apply_mask, [('output_image', 'in_file')]),
(get_brainmask, apply_mask, [('output_image', 'mask_file')]),
(get_brainmask, outputnode, [('output_image', 'out_mask')]),
- (apply_mask, outputnode, [('out_file', 'bias_corrected')]),
- (inu_n4, outputnode, [('bias_image', 'bias_image')]),
+ (apply_mask, outputnode, [('out_file', 'out_file')]),
+ (inu_n4, outputnode, [('output_image', 'bias_corrected'),
+ ('bias_image', 'bias_image')]),
])
if use_laplacian:
