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FIX: bugs in dwi workflow #1147

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merged 1 commit into from
Oct 13, 2023
Merged

FIX: bugs in dwi workflow #1147

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1 change: 0 additions & 1 deletion mriqc/interfaces/diffusion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -274,7 +274,6 @@ def _run_interface(self, runtime):

if isdefined(self.inputs.brainmask_file):
bmask = np.asanyarray(nb.load(self.inputs.brainmask_file).dataobj) > 1e-3

global_signal = np.array([
np.median(data[..., n_b0][bmask]) for n_b0 in range(img.shape[-1])
]).astype("float32")
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3 changes: 1 addition & 2 deletions mriqc/workflows/diffusion/base.py
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Expand Up @@ -196,7 +196,7 @@ def dmri_qc_workflow(name="dwiMRIQC"):
(datalad_get, iqmswf, [("in_file", "inputnode.in_file")]),
(datalad_get, sanitize, [("in_file", "in_file")]),
(sanitize, dwi_reference_wf, [("out_file", "inputnode.in_file")]),
(get_shells, dwi_reference_wf, [(("b_masks", _first), "inputnode.t_mask")]),
(shells, dwi_reference_wf, [(("b_masks", _first), "inputnode.t_mask")]),
(meta, shells, [("out_bval_file", "in_bvals")]),
(sanitize, drift, [("out_file", "full_epi")]),
(shells, get_shells, [("b_indices", "b0_ixs")]),
Expand Down Expand Up @@ -473,7 +473,6 @@ def init_dmriref_wf(
# fmt: off
workflow.connect([
(inputnode, val_bold, [("in_file", "in_file")]),
(val_bold, gen_avg, [("out_file", "in_file")]),
(inputnode, gen_avg, [("t_mask", "t_mask")]),
(val_bold, gen_avg, [("out_file", "in_file")]),
(gen_avg, outputnode, [("out_file", "ref_file")]),
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