From 6cd81e902fc5ed5d6d9b268114d2c3e359758224 Mon Sep 17 00:00:00 2001 From: David Meunier Date: Tue, 26 Mar 2024 16:53:09 +0100 Subject: [PATCH 1/4] saving transfo and padded images --- macapype/pipelines/rename.py | 74 ++++++++++++++++++++++++++++++++++++ 1 file changed, 74 insertions(+) diff --git a/macapype/pipelines/rename.py b/macapype/pipelines/rename.py index d808b7019..82149e37f 100644 --- a/macapype/pipelines/rename.py +++ b/macapype/pipelines/rename.py @@ -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_padded_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_padded_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): From 73ee512165ac7f152c7e2ad101b9495ef4afcc5f Mon Sep 17 00:00:00 2001 From: David Meunier Date: Tue, 26 Mar 2024 17:27:32 +0100 Subject: [PATCH 2/4] resample_pad --- macapype/pipelines/prepare.py | 42 ++++++++++++++++++++++++++--------- 1 file changed, 31 insertions(+), 11 deletions(-) diff --git a/macapype/pipelines/prepare.py b/macapype/pipelines/prepare.py index 2a7310b95..ae55494c1 100644 --- a/macapype/pipelines/prepare.py +++ b/macapype/pipelines/prepare.py @@ -663,25 +663,33 @@ 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( - av_T2, 'avg_img', + align_T2_on_T1, "res_file", resample_T2_pad, "flo_file") + else: + data_preparation_pipe.connect( + align_T2_on_T1, "out_file", + resample_T2_pad, "flo_file") + + data_preparation_pipe.connect( + av_T2, 'outputnode.std_img', + resample_T2_pad, "flo_file") + if "padded_template_head" in params_template.keys(): resample_T1_pad.inputs.ref_file = \ params_template["padded_template_head"] @@ -725,13 +733,25 @@ 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 From a033fec4d4f74a56674643e24ad440ff557ebacd Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 27 Mar 2024 09:54:55 +0100 Subject: [PATCH 3/4] flo_file --- macapype/pipelines/prepare.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/macapype/pipelines/prepare.py b/macapype/pipelines/prepare.py index ae55494c1..67cf369b5 100644 --- a/macapype/pipelines/prepare.py +++ b/macapype/pipelines/prepare.py @@ -686,10 +686,6 @@ def create_short_preparation_pipe(params, params_template={}, align_T2_on_T1, "out_file", resample_T2_pad, "flo_file") - data_preparation_pipe.connect( - av_T2, 'outputnode.std_img', - resample_T2_pad, "flo_file") - if "padded_template_head" in params_template.keys(): resample_T1_pad.inputs.ref_file = \ params_template["padded_template_head"] From 61b085cc20b9f2aef9c016ae81801534fb2a6a1f Mon Sep 17 00:00:00 2001 From: David Meunier Date: Wed, 27 Mar 2024 10:02:58 +0100 Subject: [PATCH 4/4] desc-pad --- macapype/pipelines/rename.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/macapype/pipelines/rename.py b/macapype/pipelines/rename.py index 82149e37f..5080d5418 100644 --- a/macapype/pipelines/rename.py +++ b/macapype/pipelines/rename.py @@ -87,7 +87,7 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe, niu.Rename(), name="rename_stereo_padded_T1") rename_stereo_padded_T1.inputs.format_string = \ - pref_deriv + "_space-stereo_padded_T1w" + pref_deriv + "_space-stereo_desc-pad_T1w" rename_stereo_padded_T1.inputs.parse_string = parse_str rename_stereo_padded_T1.inputs.keep_ext = True @@ -106,7 +106,7 @@ def rename_all_brain_derivatives(params, main_workflow, segment_pnh_pipe, niu.Rename(), name="rename_stereo_padded_T2") rename_stereo_padded_T2.inputs.format_string = \ - pref_deriv + "_space-stereo_padded_T2w" + pref_deriv + "_space-stereo_desc-pad_T2w" rename_stereo_padded_T2.inputs.parse_string = parse_str rename_stereo_padded_T2.inputs.keep_ext = True