roll back header copy
@@ -32,7 +32,6 @@ quality-assessment-protocol/blob/master/qap/anatomical_preproc.py#L105>`_.
ants.N4BiasFieldCorrection(dimension=3, save_bias=True, num_threads=n4_nthreads),
n_procs=n4_nthreads,
name='inu_n4')
- orig_hdr = pe.Node(CopyHeader(), name='orig_hdr')
sstrip = pe.Node(afni.SkullStrip(outputtype='NIFTI_GZ'), name='skullstrip')
sstrip_orig_vol = pe.Node(afni.Calc(
@@ -44,8 +43,7 @@ quality-assessment-protocol/blob/master/qap/anatomical_preproc.py#L105>`_.
inu_uni_0 = pe.Node(afni.Unifize(), name='Unifize_pre_skullstrip')
inu_uni_1 = pe.Node(afni.Unifize(gm=True), name='Unifize_post_skullstrip')
workflow.connect([
- (inu_n4, orig_hdr, [('output_image', 'in_file')]),
- (orig_hdr, inu_uni_0, [('out_file', 'in_file')]),
+ (inu_n4, inu_uni_0, [('output_image', 'in_file')]),
(inu_uni_0, sstrip, [('out_file', 'in_file')]),
(sstrip_orig_vol, inu_uni_1, [('out_file', 'in_file')]),
(inu_uni_1, outputnode, [('out_file', 'out_file')]),
@@ -53,18 +51,16 @@ quality-assessment-protocol/blob/master/qap/anatomical_preproc.py#L105>`_.
])
else:
workflow.connect([
- (inu_n4, orig_hdr, [('output_image', 'in_file')]),
- (orig_hdr, sstrip, [('out_file', 'in_file')]),
+ (inu_n4, sstrip, [('output_image', 'in_file')]),
(sstrip, sstrip_orig_vol, [('out_file', 'in_file_b')]),
(sstrip_orig_vol, outputnode, [('out_file', 'out_file')]),
- (orig_hdr, outputnode, [('out_file', 'bias_corrected')]),
+ (inu_n4, outputnode, [('output_image', 'bias_corrected')]),
])
# Remaining connections
workflow.connect([
(inputnode, sstrip_orig_vol, [('in_file', 'in_file_a')]),
- (inputnode, orig_hdr, [('in_file', 'hdr_file')]),
(inputnode, inu_n4, [('in_file', 'input_image')]),
(sstrip_orig_vol, binarize, [('out_file', 'in_file')]),
(binarize, outputnode, [('out_file', 'out_mask')]),
