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[FIX] only calc subject registration images when necessary #862

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merged 2 commits into from
Aug 16, 2022
Merged

[FIX] only calc subject registration images when necessary #862

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0083674
[FIX] only calc subject registration images when necessary
36000 Aug 2, 2022
bffa1c8
ITK map should not be generating warped b0
36000 Aug 2, 2022
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10 changes: 9 additions & 1 deletion AFQ/definitions/mapping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,10 +273,18 @@ def get_for_subses(self, base_fname, dwi, bids_info, reg_subject,
"TransformParameters"])[9:]
their_prealign[3, 3] = 1.0
warp_f5.close()
return reg.read_mapping(
mapping = reg.read_mapping(
their_disp, dwi,
reg_template, prealign=their_prealign)

def transform(self, data, **kwargs):
raise NotImplementedError(
"ITK based mappings can currently"
+ " only transform from template to subject space")

mapping.transform = transform
return mapping


class GeneratedMapMixin(object):
"""
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10 changes: 5 additions & 5 deletions AFQ/tasks/mapping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,10 +204,10 @@ def get_reg_subject(data_imap, bids_info, base_fname, dwi,
"reg_subject must be a str, ImageDefinition, or Nifti1Image")

filename_dict = {
"b0": data_imap["b0"],
"power_map": data_imap["pmap"],
"dti_fa_subject": data_imap["dti_fa"],
"subject_sls": data_imap["b0"],
"b0": "b0",
"power_map": "pmap",
"dti_fa_subject": "dti_fa",
"subject_sls": "b0",
}
bm = nib.load(data_imap["brain_mask"])

Expand All @@ -222,7 +222,7 @@ def get_reg_subject(data_imap, bids_info, base_fname, dwi,
data_imap=data_imap)
else:
if reg_subject_spec in filename_dict:
reg_subject_spec = filename_dict[reg_subject_spec]
reg_subject_spec = data_imap[filename_dict[reg_subject_spec]]
img = nib.load(reg_subject_spec)
bm = bm.get_fdata().astype(bool)
masked_data = img.get_fdata()
Expand Down