Save padded t1 t2 and transfo in derivatives (#256)

* saving transfo and padded images
Macatools · Mar 28, 2024 · 22265f1 · 22265f1
1 parent 303fa7b
commit 22265f1
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Showing 2 changed files with 101 additions and 11 deletions.
diff --git a/macapype/pipelines/prepare.py b/macapype/pipelines/prepare.py
@@ -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():
@@ -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
 

diff --git 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_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):