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