Some minor corrections (#265)

* keep_gcc_bin_mask

* IsoSurface gcc

* crop_T1 as optionnal before crop_aladin

* relaunching with curl modif

* crop_T1 and crop_aladin for ANTS_T1

macapype/nodes/pad.py

@@ -16,57 +16,28 @@ def pad_back(seg_pipe, data_preparation_pipe, inputnode,
     pad_nodename = "pad_" + outputnodefile
 
     if "short_preparation_pipe" in params.keys():
-        if "crop_T1" in params["short_preparation_pipe"].keys():
 
-            print("Padding mask in native space")
-            pad_node = pe.Node(
-                niu.Function(
-                    input_names=[
-                        'cropped_img_file',
-                        'orig_img_file',
-                        'indiv_crop'],
-                    output_names=['padded_img_file'],
-                    function=padding_cropped_img),
-                name=pad_nodename)
-
-            seg_pipe.connect(
-                node, nodefile,
-                pad_node, "cropped_img_file")
-
-            seg_pipe.connect(
-                data_preparation_pipe, "outputnode.native_T1",
-                pad_node, "orig_img_file")
+        print("Using reg_aladin transfo to pad mask back")
+        pad_node = pe.Node(
+            RegResample(inter_val="NN"),
+            name=pad_nodename)
 
-            seg_pipe.connect(
-                inputnode, "indiv_params",
-                pad_node, "indiv_crop")
-
-            seg_pipe.connect(
-                pad_node, "padded_img_file",
-                outputnode, outputnodefile)
-
-        else:
-            print("Using reg_aladin transfo to pad mask back")
-            pad_node = pe.Node(
-                RegResample(inter_val="NN"),
-                name=pad_nodename)
+        seg_pipe.connect(
+            node, nodefile,
+            pad_node, "flo_file")
 
-            seg_pipe.connect(
-                node, nodefile,
-                pad_node, "flo_file")
+        seg_pipe.connect(
+            data_preparation_pipe, "outputnode.native_T1",
+            pad_node, "ref_file")
 
-            seg_pipe.connect(
-                data_preparation_pipe, "outputnode.native_T1",
-                pad_node, "ref_file")
+        seg_pipe.connect(
+            data_preparation_pipe, "inv_tranfo.out_file",
+            pad_node, "trans_file")
 
-            seg_pipe.connect(
-                data_preparation_pipe, "inv_tranfo.out_file",
-                pad_node, "trans_file")
-
-            # outputnode
-            seg_pipe.connect(
-                pad_node, "out_file",
-                outputnode, outputnodefile)
+        # outputnode
+        seg_pipe.connect(
+            pad_node, "out_file",
+            outputnode, outputnodefile)
 
     elif "long_single_preparation_pipe" in params.keys():
         if "prep_T1" in params["long_single_preparation_pipe"].keys():

macapype/nodes/surface.py

@@ -1,13 +1,10 @@
-from nipype.interfaces.base import TraitedSpec, SimpleInterface
-from nipype.interfaces.base import traits, File
+from nipype.interfaces.base import (TraitedSpec, SimpleInterface, traits, File)
 
 
 def keep_gcc(nii_file):
-
     import os
     import nibabel as nib
     import numpy as np
-
     from nipype.utils.filemanip import split_filename as split_f
 
     def getLargestCC(segmentation):
@@ -28,8 +25,6 @@ def getLargestCC(segmentation):
     data[data > 0] = 1
     binary = np.array(data, dtype="bool")
 
-    # skimage
-
     # skimage GCC
     new_data = getLargestCC(binary)
 
@@ -135,8 +130,8 @@ def wrap_afni_IsoSurface(nii_file):
     remesh = 0.5
 
     # Tsmooth
-    KPB = 0.1
-    NITER = 100
+    KPB = 0.0001
+    NITER = 10000
 
     # remesh
     remesh = 0.5