def _run_interface(self, runtime): if self.inputs.subjects_dir: os.environ.update({'SUBJECTS_DIR': self.inputs.subjects_dir}) if not os.path.exists(op.join(self.inputs.subjects_dir, self.inputs.subject_id)): raise Exception iflogger.info("ROI_HR_th.nii.gz / fsmask_1mm.nii.gz CREATION") iflogger.info("=============================================") create_annot_label(self.inputs.subject_id, self.inputs.subjects_dir, self.inputs.freesurfer_dir, self.inputs.parcellation_name) create_roi(self.inputs.subject_id, self.inputs.subjects_dir, self.inputs.freesurfer_dir, self.inputs.parcellation_name, self.inputs.dilation) create_wm_mask(self.inputs.subject_id, self.inputs.subjects_dir, self.inputs.freesurfer_dir, self.inputs.parcellation_name) crop_and_move_datasets(self.inputs.subject_id, self.inputs.subjects_dir, self.inputs.freesurfer_dir, self.inputs.parcellation_name, self.inputs.out_roi_file, self.inputs.dilation) return runtime
def _run_interface(self, runtime): #if self.inputs.subjects_dir: # os.environ.update({'SUBJECTS_DIR': self.inputs.subjects_dir}) iflogger.info("ROI_HR_th.nii.gz / fsmask_1mm.nii.gz CREATION") iflogger.info("=============================================") if self.inputs.parcellation_scheme == "Lausanne2008": create_T1_and_Brain(self.inputs.subject_id, self.inputs.subjects_dir) create_annot_label(self.inputs.subject_id, self.inputs.subjects_dir) create_roi(self.inputs.subject_id, self.inputs.subjects_dir) create_wm_mask(self.inputs.subject_id, self.inputs.subjects_dir) if self.inputs.erode_masks: erode_mask( op.join(self.inputs.subjects_dir, self.inputs.subject_id, 'mri', 'fsmask_1mm.nii.gz')) erode_mask( op.join(self.inputs.subjects_dir, self.inputs.subject_id, 'mri', 'csf_mask.nii.gz')) erode_mask( op.join(self.inputs.subjects_dir, self.inputs.subject_id, 'mri', 'brainmask.nii.gz')) crop_and_move_datasets(self.inputs.subject_id, self.inputs.subjects_dir) if self.inputs.parcellation_scheme == "NativeFreesurfer": create_T1_and_Brain(self.inputs.subject_id, self.inputs.subjects_dir) generate_WM_and_GM_mask(self.inputs.subject_id, self.inputs.subjects_dir) if self.inputs.erode_masks: erode_mask( op.join(self.inputs.subjects_dir, self.inputs.subject_id, 'mri', 'fsmask_1mm.nii.gz')) erode_mask( op.join(self.inputs.subjects_dir, self.inputs.subject_id, 'mri', 'csf_mask.nii.gz')) erode_mask( op.join(self.inputs.subjects_dir, self.inputs.subject_id, 'mri', 'brainmask.nii.gz')) crop_and_move_WM_and_GM(self.inputs.subject_id, self.inputs.subjects_dir) return runtime
def _run_interface(self, runtime): #if self.inputs.subjects_dir: # os.environ.update({'SUBJECTS_DIR': self.inputs.subjects_dir}) iflogger.info("ROI_HR_th.nii.gz / fsmask_1mm.nii.gz CREATION") iflogger.info("=============================================") if self.inputs.parcellation_scheme == "Lausanne2008": create_annot_label(self.inputs.subject_id, self.inputs.subjects_dir) create_roi(self.inputs.subject_id, self.inputs.subjects_dir) create_wm_mask(self.inputs.subject_id, self.inputs.subjects_dir) if self.inputs.erode_masks: erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,'mri','fsmask_1mm.nii.gz')) erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,'mri','csf_mask.nii.gz')) erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,'mri','brainmask.nii.gz')) crop_and_move_datasets(self.inputs.subject_id, self.inputs.subjects_dir) if self.inputs.parcellation_scheme == "NativeFreesurfer": generate_WM_and_GM_mask(self.inputs.subject_id, self.inputs.subjects_dir) if self.inputs.erode_masks: erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,'mri','fsmask_1mm.nii.gz')) erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,'mri','csf_mask.nii.gz')) erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,'mri','brainmask.nii.gz')) crop_and_move_WM_and_GM(self.inputs.subject_id, self.inputs.subjects_dir) return runtime