diff --git a/pymialsrtk/interfaces/preprocess.py b/pymialsrtk/interfaces/preprocess.py index 5c6dabe0a..c1a02343c 100644 --- a/pymialsrtk/interfaces/preprocess.py +++ b/pymialsrtk/interfaces/preprocess.py @@ -1368,7 +1368,8 @@ def _compute_motion_index(self, in_file): img = nibabel.load(in_file) - voxelspacing = img.header['pixdim'][2] + # Todo: Compute centroid displacement as a distance instead of a number of voxel + # voxelspacing = img.header['pixdim'][2] data = img.get_fdata() z = np.where(data)[2] diff --git a/pymialsrtk/interfaces/reconstruction.py b/pymialsrtk/interfaces/reconstruction.py index 4e445b00b..c6284cf9b 100644 --- a/pymialsrtk/interfaces/reconstruction.py +++ b/pymialsrtk/interfaces/reconstruction.py @@ -376,7 +376,8 @@ def _run_interface(self, runtime): cmd += ['--outer-thresh', str(self.inputs.in_outer_thresh)] # JSON file SRTV - self.m_output_dict["Description"] = "Isotropic high-resolution image reconstructed using the Total-Variation Super-Resolution algorithm provided by MIALSRTK" + self.m_output_dict["Description"] = "Isotropic high-resolution image reconstructed using the Total-Variation" \ + " Super-Resolution algorithm provided by MIALSRTK" self.m_output_dict["Input sources run order"] = self.inputs.stacks_order self.m_output_dict["CustomMetaData"] = {} self.m_output_dict["CustomMetaData"]["Number of scans used"] = str(len(self.inputs.stacks_order)) diff --git a/pymialsrtk/pipelines/anatomical/srr.py b/pymialsrtk/pipelines/anatomical/srr.py index 78be2821e..b7373ae3e 100644 --- a/pymialsrtk/pipelines/anatomical/srr.py +++ b/pymialsrtk/pipelines/anatomical/srr.py @@ -320,8 +320,6 @@ def create_workflow(self): srtkTVSuperResolution.inputs.in_lambda = self.lambdaTV srtkTVSuperResolution.inputs.use_manual_masks = self.use_manual_masks - srTVdictSink = Node(JSONFileSink(),name='srtv_json_sinker') - srtkRefineHRMaskByIntersection = Node(interface=postprocess.MialsrtkRefineHRMaskByIntersection(), name='srtkRefineHRMaskByIntersection') srtkRefineHRMaskByIntersection.inputs.bids_dir = self.bids_dir @@ -408,9 +406,6 @@ def create_workflow(self): self.wf.connect(srtkImageReconstruction, ("output_transforms", utils.sort_ascending), srtkRefineHRMaskByIntersection, "input_transforms") self.wf.connect(srtkTVSuperResolution, "output_sr", srtkRefineHRMaskByIntersection, "input_sr") - # self.wf.connect(srtkTVSuperResolution, "output_dict", srTVdictSink, "in_dict") - # self.wf.connect(srtkTVSuperResolution, "output_json_path", srTVdictSink, "out_file") - self.wf.connect(srtkTVSuperResolution, "output_sr", srtkMaskImage02, "in_file") self.wf.connect(srtkRefineHRMaskByIntersection, "output_srmask", srtkMaskImage02, "in_mask") @@ -427,7 +422,6 @@ def create_workflow(self): self.wf.connect(srtkImageReconstruction, "output_sdi", datasink, 'anat.@SDI') self.wf.connect(srtkN4BiasFieldCorrection, "output_image", datasink, 'anat.@SR') - # self.wf.connect(srTVdictSink, "out_file", datasink, 'anat.@SRjson') self.wf.connect(srtkTVSuperResolution, "output_json_path", datasink, 'anat.@SRjson') self.wf.connect(srtkRefineHRMaskByIntersection, "output_srmask", datasink, 'anat.@SRmask')