def flip_if_needed(data_selection, nii_path, ind,
output_filename='flipped.nii.gz',
):
"""Check based on a SAMRI data selection of Bruker Paravision scans, if the orientation is incorrect (“Prone”, terminologically correct, but corresponding to an incorrect “Supine” representation in Bruker ParaVision small animal scans), and flip the scan with respect to the axial axis if so.
Parameters
----------
data_selection : pandas.DataFrame
Pandas Dataframe object, with indices corresponding to the SAMRI data source iterator and columns including 'PV_position'.
nii_path : str
Path to a NIfTI file.
ind : int
Index of the `data_selection` entry.
output_filename : str, optional
String specifying the desired flipped NIfTI filename for potential flipped output.
"""
from os import path
from samri.manipulations import flip_axis
position = data_selection.iloc[ind]['PV_position']
output_filename = path.abspath(path.expanduser(output_filename))
nii_path = path.abspath(path.expanduser(nii_path))
# The output_filename variable may not contain a format suffix, as it is used to generate associated files.
if output_filename[-7:] != '.nii.gz' and output_filename[-4:] != '.nii':
output_filename = '{}.nii.gz'.format(output_filename)
if position == 'Prone':
output_filename = flip_axis(nii_path, axis=2, out_path=output_filename)
else:
output_filename = nii_path
return output_filename
def test_flip_axis():
nii_path = '/usr/share/samri_bidsdata/bids_collapsed/sub-4007/ses-ofM/func/sub-4007_ses-ofM_task-JogB_acq-EPIlowcov_run-0_bold.nii.gz'
flip_axis(nii_path)