def _run_interface(self, runtime):
target_brain = fsl.Info.standard_image("avg152T1_brain.nii.gz")
m = Mosaic(self.inputs.in_file, target_brain)
m.plot_contours("Reds", 2)
m.savefig("warp_report.png")
m.close()
return runtime
def _run_interface(self, runtime):
target_brain = fsl.Info.standard_image("avg152T1_brain.nii.gz")
m = Mosaic(self.inputs.in_file, target_brain)
m.plot_contours("Reds", 2)
m.savefig("warp_report.png")
m.close()
return runtime
def _run_interface(self, runtime):
subjects_dir = os.environ["SUBJECTS_DIR"]
wm_file = op.join(subjects_dir, self.inputs.subject_id, "mri/wm.mgz")
wm_data = nib.load(wm_file).get_data().astype(bool).astype(int)
m = Mosaic(self.inputs.in_file, wm_data, step=3)
m.plot_contours(["#DD2222"])
m.savefig("func2anat.png")
m.close()
return runtime
def _run_interface(self, runtime):
subjects_dir = os.environ["SUBJECTS_DIR"]
wm_file = op.join(subjects_dir, self.inputs.subject_id, "mri/wm.mgz")
wm_data = nib.load(wm_file).get_data().astype(bool).astype(int)
m = Mosaic(self.inputs.in_file, wm_data, step=3)
m.plot_contours(["#DD2222"])
m.savefig("func2anat.png")
m.close()
return runtime