Modif real params (#259)

* saving full cmd in real_params.json  + solved some bugs

macapype/pipelines/full_pipelines.py

@@ -932,7 +932,7 @@ def create_full_ants_subpipes(
     seg_pipe.connect(data_preparation_pipe, 'outputnode.preproc_T1',
                      outputnode, "stereo_T1")
 
-    seg_pipe.connect(data_preparation_pipe, 'outputnode.preproc_T1',
+    seg_pipe.connect(data_preparation_pipe, 'outputnode.preproc_T2',
                      outputnode, "stereo_T2")
 
     seg_pipe.connect(data_preparation_pipe, "outputnode.stereo_padded_T1",
@@ -1103,46 +1103,54 @@ def create_full_ants_subpipes(
     if mask_file is None:
 
         # full extract brain pipeline (correct_bias, denoising, extract brain)
-        if "extract_pipe" not in params.keys():
-            return seg_pipe
+        if "extract_pipe" in params.keys():
 
-        # brain extraction
-        extract_pipe = create_extract_pipe(
-            params_template=params_template,
-            params=parse_key(params, "extract_pipe"))
+            # brain extraction
+            extract_pipe = create_extract_pipe(
+                params_template=params_template,
+                params=parse_key(params, "extract_pipe"))
 
-        seg_pipe.connect(inputnode, "indiv_params",
-                                    extract_pipe, "inputnode.indiv_params")
+            seg_pipe.connect(inputnode, "indiv_params",
+                                        extract_pipe, "inputnode.indiv_params")
 
-        if "correct_bias_pipe" in params:
-            seg_pipe.connect(correct_bias_pipe,
-                             "outputnode.debiased_T1",
-                             extract_pipe, "inputnode.restore_T1")
+            if "correct_bias_pipe" in params:
+                seg_pipe.connect(
+                    correct_bias_pipe, "outputnode.debiased_T1",
+                    extract_pipe, "inputnode.restore_T1")
 
-        elif "N4debias" in params.keys():
-            # brain extraction
-            seg_pipe.connect(N4debias_T1, "output_image",
-                             extract_pipe, "inputnode.restore_T1")
+            elif "N4debias" in params.keys():
+                # brain extraction
+                seg_pipe.connect(
+                    N4debias_T1, "output_image",
+                    extract_pipe, "inputnode.restore_T1")
 
-        elif "fast" in params.keys():
+            elif "fast" in params.keys():
 
-            # brain extraction
-            seg_pipe.connect(fast_T1, ("restored_image", show_files),
-                             extract_pipe, "inputnode.restore_T1")
-        else:
+                # brain extraction
+                seg_pipe.connect(
+                    fast_T1, ("restored_image", show_files),
+                    extract_pipe, "inputnode.restore_T1")
+            else:
 
-            seg_pipe.connect(data_preparation_pipe, 'outputnode.preproc_T1',
-                             extract_pipe, "inputnode.restore_T1")
+                seg_pipe.connect(
+                    data_preparation_pipe, 'outputnode.preproc_T1',
+                    extract_pipe, "inputnode.restore_T1")
 
-        # outputnode
-        seg_pipe.connect(extract_pipe, "smooth_mask.out_file",
-                         outputnode, "stereo_brain_mask")
-
-        if pad:
-            pad_back(
-                seg_pipe, data_preparation_pipe, inputnode,
+            # outputnode
+            seg_pipe.connect(
                 extract_pipe, "smooth_mask.out_file",
-                outputnode, "native_brain_mask", params)
+                outputnode, "stereo_brain_mask")
+
+            if pad:
+                pad_back(
+                    seg_pipe, data_preparation_pipe, inputnode,
+                    extract_pipe, "smooth_mask.out_file",
+                    outputnode, "native_brain_mask", params)
+
+        # full extract brain pipeline (correct_bias, denoising, extract brain)
+        else:
+            print("no extract_brain method is defined, skipping")
+            return seg_pipe
 
     else:
         print("Using native external mask {}".format(mask_file))
@@ -1268,9 +1276,23 @@ def create_full_ants_subpipes(
                              debias, 't2_file')
 
         if mask_file is None:
-            seg_pipe.connect(
-                extract_pipe, "smooth_mask.out_file",
-                debias, 'b')
+            if "extract_pipe" in params.keys():
+                seg_pipe.connect(
+                    extract_pipe, "smooth_mask.out_file",
+                    debias, 'b')
+            else:
+                debias.inputs.bet = 1
+
+                # outputnode
+                seg_pipe.connect(
+                    debias, "debiased_mask_file",
+                    outputnode, "stereo_brain_mask")
+
+                if pad:
+                    pad_back(
+                        seg_pipe, data_preparation_pipe, inputnode,
+                        debias, "debiased_mask_file",
+                        outputnode, "native_brain_mask", params)
 
         else:
             seg_pipe.connect(
@@ -1340,13 +1362,14 @@ def create_full_ants_subpipes(
                              restore_mask_T2, 'in_file')
 
         if mask_file is None:
-            seg_pipe.connect(
-                extract_pipe, "smooth_mask.out_file",
-                restore_mask_T1, 'mask_file')
-
-            seg_pipe.connect(
-                extract_pipe, "smooth_mask.out_file",
-                restore_mask_T2, 'mask_file')
+            if "extract_pipe" in params.keys():
+                seg_pipe.connect(
+                    extract_pipe, "smooth_mask.out_file",
+                    restore_mask_T1, 'mask_file')
+
+                seg_pipe.connect(
+                    extract_pipe, "smooth_mask.out_file",
+                    restore_mask_T2, 'mask_file')
         else:
             seg_pipe.connect(
                 apply_crop_external_mask, "out_file",

macapype/utils/subs.json

@@ -31,7 +31,7 @@
     "_restore_brain": "",
     "_restore":"",
     "_noise_corrected":"",
-    "_brain_corrected":"",
+    "_brain":"",
     "_corrected":"",
     "_maths":"",
     "_masked":"",

setup.py

@@ -7,8 +7,8 @@
 
 required_packages = [
     "nipype", "nilearn", "networkx",
-    "pybids", "scikit-image", "nibabel==3.2.2",
-    "numpy==1.22", "brain-slam"]
+    "pybids", "scikit-image", "nibabel==4.0.0",
+    "numpy==1.23", "brain-slam"]
 
 verstr = "unknown"
 try:

workflows/segment_pnh.py

@@ -43,6 +43,7 @@
 #           Kepkee Loh ([email protected])
 #           Julien Sein ([email protected])
 
+import sys
 import os
 import os.path as op
 
@@ -80,7 +81,7 @@
 ###############################################################################
 
 
-def create_main_workflow(data_dir, process_dir, soft, species, datatypes,
+def create_main_workflow(cmd, data_dir, process_dir, soft, species, datatypes,
                          subjects, sessions, acquisitions, reconstructions,
                          params_file, indiv_params_file, mask_file,
                          template_path, template_files, nprocs, reorient,
@@ -455,6 +456,8 @@ def create_main_workflow(data_dir, process_dir, soft, species, datatypes,
     # saving real params.json
     params["macapype_version"] = __version__
 
+    params["full_command"] = cmd
+
     real_params_file = op.join(process_dir, wf_name, "real_params.json")
     with open(real_params_file, 'w+') as fp:
         json.dump(params, fp)
@@ -553,9 +556,12 @@ def main():
 
     args = parser.parse_args()
 
+    cmd = " ".join(sys.argv)
+
     # main_workflow
     print("Initialising the pipeline...")
     create_main_workflow(
+        cmd=cmd,
         data_dir=args.data,
         soft=args.soft,
         process_dir=args.out,