def convert_to_nii(self, in_files: list, target_dir: Path):
"""
Convert MRTrix's .mif format to NIfTI for compatability with FSL's
functions.
Parameters
----------
in_files : list
List of files to convert
target_dir : Path
Path of directory of converted files
"""
target_dir = target_dir / "anatomical"
target_dir.mkdir(exist_ok=True)
out_files = []
for in_file, session in zip(in_files, self.sessions):
out_fname = f"{in_file.name.split('.')[0]}_{session}.nii.gz"
out_file = target_dir / out_fname
if out_file.exists():
message = messages.FILE_EXISTS.format(fname=out_file)
message = colored(message, "yellow")
warnings.warn(message)
else:
executer = conversions.mrtrix_conversion({"nii": in_file},
out_file)
message = messages.CONVERT_TO_NII.format(
in_file=in_file,
out_file=out_file,
command=executer.cmdline,
)
message = colored(message, "green")
print(message)
executer.run()
out_files.append(out_file)
self.registrations_dict[session]["anatomical"] = out_file
def apply_xfm_to_mifs(
in_file: Path,
aff: Path,
ref: Path,
target_dir: Path,
):
"""
Apply pre-calculated transformation matrix to numerous image files.
Parameters
----------
in_files : list
A list of paths to images to be registered
aff : Path
Path to pre-calculated transformation matrix
target_dir : Path
Path to output directory
keep_tmps : bool, optional
Whether to keep intermidiate files, by default False
"""
out_nii = target_dir / f"{in_file.name.split('.')[0]}_tmp.nii.gz"
out_registered = target_dir / f"{in_file.name.split('.')[0]}.nii.gz"
if not out_registered.exists():
mrconvert = mrtrix_conversion({"nii": in_file}, out_nii)
mrconvert.run()
executer = apply_xfm(out_nii, ref, aff, out_registered)
else:
executer = None
return executer, out_nii, out_registered
def convert_format(
self,
session: str,
session_dict: dict,
target_dir: Path,
):
"""
Convert NIfTI files to .mif format for compatability with MRTrix3's
commands.
Parameters
----------
session : str
key representing a session within the dataset
session_dict : dict
Dictionary containing paths to session-relevant files
target_dir : Path
Path to user-defined session's output directory
"""
for modality, vals in session_dict.items():
target_file = target_dir / f"{modality}.mif"
if target_file.exists():
message = messages.FILE_EXISTS.format(fname=target_file)
message = colored(message, "yellow")
warnings.warn(message)
else:
converter = conversions.mrtrix_conversion(vals, target_file)
message = messages.CONVERT_TO_MIF.format(
in_file=vals.get("nii"),
out_file=target_file,
command=converter.cmdline,
)
message = colored(message, "green")
print(message)
converter.run()
self.output_dict[session][f"{modality}_mif"] = target_file