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Remove unused identity transform from anatomical derivatives #851

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tsalo opened this issue Nov 8, 2024 · 2 comments
Open

Remove unused identity transform from anatomical derivatives #851

tsalo opened this issue Nov 8, 2024 · 2 comments
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@tsalo
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tsalo commented Nov 8, 2024

Summary

The file is named sub-PNC/anat/sub-PNC_from-orig_to-T1w_mode-image_xfm.txt.

@tsalo tsalo added the bug Something isn't working label Nov 8, 2024
@tsalo
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tsalo commented Nov 8, 2024

Here's the relevant section of code:

if num_images == 1:
def _get_first(in_list):
if isinstance(in_list, (list, tuple)):
return in_list[0]
return in_list
n4_correct = pe.Node(n4_interface, name="n4_correct", n_procs=omp_nthreads)
outputnode.inputs.template_transforms = [pkgr("qsiprep", "data/itkIdentityTransform.txt")]
workflow.connect([
(anat_conform, outputnode, [
(('out_file', _get_first), 'template')]),
(anat_conform, n4_correct, [
(('out_file', _get_first), 'input_image')]),
(n4_correct, outputnode, [('output_image', 'bias_corrected')])
]) # fmt:skip
return workflow

I think what we need is individual T1w/T2w image-to-combined T1w/T2w image transforms, which isn't really captured here.

@tsalo
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tsalo commented Nov 11, 2024

fMRIPrep will write out orig-to-T1w transforms if there are multiple T1ws across sessions (not sure what happens where there are multiple T1ws in a single session), but it won't write them out if there's a single T1w, so we don't need to write out the identity transform.

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