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Save padded t1 t2 and transfo in derivatives #256

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merged 4 commits into from
Mar 28, 2024
Merged

Save padded t1 t2 and transfo in derivatives #256

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6cd81e9
saving transfo and padded images
davidmeunier79 Mar 26, 2024
73ee512
resample_pad
davidmeunier79 Mar 26, 2024
a033fec
flo_file
davidmeunier79 Mar 27, 2024
61b085c
desc-pad
davidmeunier79 Mar 27, 2024
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38 changes: 27 additions & 11 deletions macapype/pipelines/prepare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -663,23 +663,27 @@ def create_short_preparation_pipe(params, params_template={},
regutils.RegResample(),
name="resample_T2_pad")

# T1 to pad
if "avg_reorient_pipe" in params.keys():

data_preparation_pipe.connect(
av_T1, 'outputnode.std_img',
resample_T1_pad, "flo_file")

data_preparation_pipe.connect(
av_T2, 'outputnode.std_img',
resample_T2_pad, "flo_file")

else:
data_preparation_pipe.connect(
av_T1, 'avg_img',
resample_T1_pad, "flo_file")

# T2 to pad
if 'aladin_T2_on_T1' in params.keys():
data_preparation_pipe.connect(
align_T2_on_T1, "res_file",
resample_T2_pad, "flo_file")

else:
data_preparation_pipe.connect(
av_T2, 'avg_img',
align_T2_on_T1, "out_file",
resample_T2_pad, "flo_file")

if "padded_template_head" in params_template.keys():
Expand Down Expand Up @@ -725,13 +729,25 @@ def create_short_preparation_pipe(params, params_template={},
resample_T2_pad, "trans_file")

# outputnode
data_preparation_pipe.connect(
resample_T1_pad, 'out_file',
outputnode, 'stereo_padded_T1')
if "use_T2" in params.keys():

data_preparation_pipe.connect(
resample_T2_pad, 'out_file',
outputnode, 'stereo_padded_T2')
data_preparation_pipe.connect(
resample_T1_pad, 'out_file',
outputnode, 'stereo_padded_T2')

data_preparation_pipe.connect(
resample_T2_pad, 'out_file',
outputnode, 'stereo_padded_T1')

else:

data_preparation_pipe.connect(
resample_T1_pad, 'out_file',
outputnode, 'stereo_padded_T1')

data_preparation_pipe.connect(
resample_T2_pad, 'out_file',
outputnode, 'stereo_padded_T2')

return data_preparation_pipe

Expand Down
74 changes: 74 additions & 0 deletions macapype/pipelines/rename.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,80 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe,
rename_stereo_T2, 'out_file',
datasink, '@stereo_T2')

# transfo to native to template and inverse
if "crop_T1" not in params["short_preparation_pipe"].keys():

# rename trans
rename_trans = pe.Node(
niu.Rename(),
name="rename_trans")
rename_trans.inputs.format_string = \
pref_deriv + "_space-native_target-stereo_affine"
rename_trans.inputs.parse_string = parse_str
rename_trans.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.native_to_stereo_trans',
rename_trans, 'in_file')

main_workflow.connect(
rename_trans, 'out_file',
datasink, '@native_to_stereo_trans')

# rename inv_trans
rename_inv_trans = pe.Node(
niu.Rename(),
name="rename_inv_trans")
rename_inv_trans.inputs.format_string = \
pref_deriv + "_space-stereo_target-native_affine"
rename_inv_trans.inputs.parse_string = parse_str
rename_inv_trans.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.stereo_to_native_trans',
rename_inv_trans, 'in_file')

main_workflow.connect(
rename_inv_trans, 'out_file',
datasink, '@stereo_to_native_trans')

if "resample_T1_pad" in params["short_preparation_pipe"].keys():

rename_stereo_padded_T1 = pe.Node(
niu.Rename(),
name="rename_stereo_padded_T1")
rename_stereo_padded_T1.inputs.format_string = \
pref_deriv + "_space-stereo_desc-pad_T1w"
rename_stereo_padded_T1.inputs.parse_string = parse_str
rename_stereo_padded_T1.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.stereo_padded_T1',
rename_stereo_padded_T1, 'in_file')

main_workflow.connect(
rename_stereo_padded_T1, 'out_file',
datasink, '@stereo_padded_T1')

if 't2' in datatypes:

# rename stereo_padded_T2
rename_stereo_padded_T2 = pe.Node(
niu.Rename(),
name="rename_stereo_padded_T2")
rename_stereo_padded_T2.inputs.format_string = \
pref_deriv + "_space-stereo_desc-pad_T2w"
rename_stereo_padded_T2.inputs.parse_string = parse_str
rename_stereo_padded_T2.inputs.keep_ext = True

main_workflow.connect(
segment_pnh_pipe, 'outputnode.stereo_padded_T2',
rename_stereo_padded_T2, 'in_file')

main_workflow.connect(
rename_stereo_padded_T2, 'out_file',
datasink, '@stereo_padded_T2')

if ("fast" in params
or "N4debias" in params
or "correct_bias_pipe" in params):
Expand Down
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