def rename_into_caps(in_bids_dwi, fname_dwi, fname_bval, fname_bvec,
fname_brainmask):
"""
Rename the outputs of the pipelines into CAPS format namely:
<source_file>_space-T1w_preproc[.nii.gz|bval|bvec]
Args:
in_bids_dwi (str): Input BIDS DWI to extract the <source_file>
fname_dwi (str): Preprocessed DWI.
fname_bval (str): Preprocessed DWI.
fname_bvec (str): Preprocessed DWI.
fname_brainmask (str): B0 mask.
Returns:
The different outputs in CAPS format
"""
import os
from nipype.interfaces.utility import Rename
from nipype.utils.filemanip import split_filename
# Extract <source_file> in format sub-CLNC01_ses-M00_[acq-label]_dwi
_, source_file_dwi, _ = split_filename(in_bids_dwi)
# Extract base path from fname:
base_dir_dwi, _, _ = split_filename(fname_dwi)
base_dir_bval, _, _ = split_filename(fname_bval)
base_dir_bvec, _, _ = split_filename(fname_bvec)
base_dir_brainmask, _, _ = split_filename(fname_brainmask)
# Rename into CAPS DWI :
rename_dwi = Rename()
rename_dwi.inputs.in_file = fname_dwi
rename_dwi.inputs.format_string = os.path.join(
base_dir_dwi, source_file_dwi + "_space-b0_preproc.nii.gz")
out_caps_dwi = rename_dwi.run()
# Rename into CAPS bval :
rename_bval = Rename()
rename_bval.inputs.in_file = fname_bval
rename_bval.inputs.format_string = os.path.join(
base_dir_bval, source_file_dwi + "_space-b0_preproc.bval")
out_caps_bval = rename_bval.run()
# Rename into CAPS DWI :
rename_bvec = Rename()
rename_bvec.inputs.in_file = fname_bvec
rename_bvec.inputs.format_string = os.path.join(
base_dir_bvec, source_file_dwi + "_space-b0_preproc.bvec")
out_caps_bvec = rename_bvec.run()
# Rename into CAPS DWI :
rename_brainmask = Rename()
rename_brainmask.inputs.in_file = fname_brainmask
rename_brainmask.inputs.format_string = os.path.join(
base_dir_brainmask, source_file_dwi + "_space-b0_brainmask.nii.gz")
out_caps_brainmask = rename_brainmask.run()
return out_caps_dwi.outputs.out_file, out_caps_bval.outputs.out_file, \
out_caps_bvec.outputs.out_file, out_caps_brainmask.outputs.out_file
def rename_into_caps(
in_bids_pet,
fname_pet,
fname_trans,
suvr_reference_region,
uncropped_image,
fname_pet_in_t1w=None,
):
"""
Rename the outputs of the pipelines into CAPS format.
Args:
in_bids_pet (str): Input BIDS PET to extract the <source_file>
fname_pet (str): Preprocessed PET file.
fname_trans (str): Transformation file from PET to MRI space
suvr_reference_region (str): SUVR mask name for file name output
uncropped_image (bool): Pipeline argument for image cropping
fname_pet_in_t1w (bool): Pipeline argument for saving intermediate file
Returns:
The different outputs in CAPS format
"""
import os
from nipype.interfaces.utility import Rename
from nipype.utils.filemanip import split_filename
_, source_file_pet, _ = split_filename(in_bids_pet)
# Rename into CAPS PET:
rename_pet = Rename()
rename_pet.inputs.in_file = fname_pet
if not uncropped_image:
suffix = f"_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_suvr-{suvr_reference_region}_pet.nii.gz"
rename_pet.inputs.format_string = source_file_pet + suffix
else:
suffix = f"_space-MNI152NLin2009cSym_res-1x1x1_suvr-{suvr_reference_region}_pet.nii.gz"
rename_pet.inputs.format_string = source_file_pet + suffix
out_caps_pet = rename_pet.run().outputs.out_file
# Rename into CAPS transformation file:
rename_trans = Rename()
rename_trans.inputs.in_file = fname_trans
rename_trans.inputs.format_string = source_file_pet + "_space-T1w_rigid.mat"
out_caps_trans = rename_trans.run().outputs.out_file
# Rename intermediate PET in T1w MRI space
if fname_pet_in_t1w is not None:
rename_pet_in_t1w = Rename()
rename_pet_in_t1w.inputs.in_file = fname_pet_in_t1w
rename_pet_in_t1w.inputs.format_string = (source_file_pet +
"_space-T1w_pet.nii.gz")
out_caps_pet_in_t1w = rename_pet_in_t1w.run().outputs.out_file
else:
out_caps_pet_in_t1w = None
return out_caps_pet, out_caps_trans, out_caps_pet_in_t1w
def __init__(self, in_file='path', format_string='', **options):
from nipype.interfaces.utility import Rename
rename = Rename()
rename.inputs.in_file = in_file
rename.inputs.format_string = format_string
for ef in options:
setattr(rename.inputs, ef, options[ef])
self.res = rename.run()
def rename_into_caps(
in_bids_dwi,
fname_dwi,
fname_bval,
fname_bvec,
fname_brainmask,
fname_magnitude,
fname_fmap,
fname_smoothed_fmap,
):
"""Rename the outputs of the pipelines into CAPS.
Args:
in_bids_dwi (str): Input BIDS DWI to extract the <source_file>
fname_dwi (str): Preprocessed DWI file.
fname_bval (str): Preprocessed bval.
fname_bvec (str): Preprocessed bvec.
fname_brainmask (str): B0 mask.
fname_smoothed_fmap (str): Smoothed (calibrated) fmap on b0 space.
fname_fmap (str): Calibrated fmap on b0 space.
fname_magnitude (str): Magnitude image on b0 space.
Returns:
Tuple[str, str, str, str, str, str, str]: The different outputs in CAPS format.
"""
import os
from nipype.interfaces.utility import Rename
from nipype.utils.filemanip import split_filename
# Extract <source_file> in format sub-CLNC01_ses-M00_[acq-label]_dwi
_, source_file_dwi, _ = split_filename(in_bids_dwi)
# Extract base path from fname:
base_dir_dwi, _, _ = split_filename(fname_dwi)
base_dir_bval, _, _ = split_filename(fname_bval)
base_dir_bvec, _, _ = split_filename(fname_bvec)
base_dir_brainmask, _, _ = split_filename(fname_brainmask)
base_dir_smoothed_fmap, _, _ = split_filename(fname_smoothed_fmap)
base_dir_calibrated_fmap, _, _ = split_filename(fname_fmap)
base_dir_magnitude, _, _ = split_filename(fname_magnitude)
# Rename into CAPS DWI:
rename_dwi = Rename()
rename_dwi.inputs.in_file = fname_dwi
rename_dwi.inputs.format_string = os.path.join(
base_dir_dwi, f"{source_file_dwi}_space-b0_preproc.nii.gz")
out_caps_dwi = rename_dwi.run()
# Rename into CAPS bval:
rename_bval = Rename()
rename_bval.inputs.in_file = fname_bval
rename_bval.inputs.format_string = os.path.join(
base_dir_bval, f"{source_file_dwi}_space-b0_preproc.bval")
out_caps_bval = rename_bval.run()
# Rename into CAPS bvec:
rename_bvec = Rename()
rename_bvec.inputs.in_file = fname_bvec
rename_bvec.inputs.format_string = os.path.join(
base_dir_bvec, f"{source_file_dwi}_space-b0_preproc.bvec")
out_caps_bvec = rename_bvec.run()
# Rename into CAPS brainmask:
rename_brainmask = Rename()
rename_brainmask.inputs.in_file = fname_brainmask
rename_brainmask.inputs.format_string = os.path.join(
base_dir_brainmask, f"{source_file_dwi}_space-b0_brainmask.nii.gz")
out_caps_brainmask = rename_brainmask.run()
# Rename into CAPS magnitude:
rename_magnitude = Rename()
rename_magnitude.inputs.in_file = fname_magnitude
rename_magnitude.inputs.format_string = os.path.join(
base_dir_magnitude, f"{source_file_dwi}_space-b0_magnitude1.nii.gz")
out_caps_magnitude = rename_magnitude.run()
# Rename into CAPS fmap:
rename_calibrated_fmap = Rename()
rename_calibrated_fmap.inputs.in_file = fname_fmap
rename_calibrated_fmap.inputs.format_string = os.path.join(
base_dir_calibrated_fmap, f"{source_file_dwi}_space-b0_fmap.nii.gz")
out_caps_fmap = rename_calibrated_fmap.run()
# Rename into CAPS smoothed fmap:
rename_smoothed_fmap = Rename()
rename_smoothed_fmap.inputs.in_file = fname_smoothed_fmap
rename_smoothed_fmap.inputs.format_string = os.path.join(
base_dir_smoothed_fmap,
f"{source_file_dwi}_space-b0_fwhm-4_fmap.nii.gz")
out_caps_smoothed_fmap = rename_smoothed_fmap.run()
return (
out_caps_dwi.outputs.out_file,
out_caps_bval.outputs.out_file,
out_caps_bvec.outputs.out_file,
out_caps_brainmask.outputs.out_file,
out_caps_magnitude.outputs.out_file,
out_caps_fmap.outputs.out_file,
out_caps_smoothed_fmap.outputs.out_file,
)
def rename_into_caps(
in_caps_dwi,
in_norm_fa,
in_norm_md,
in_norm_ad,
in_norm_rd,
in_b_spline_transform,
in_affine_matrix,
):
"""Rename different outputs of the pipelines into CAPS format.
Returns:
The different outputs with CAPS naming convention
"""
from nipype.interfaces.utility import Rename
from clinica.pipelines.dwi_dti.dwi_dti_utils import (
extract_bids_identifier_from_caps_filename, )
bids_identifier = extract_bids_identifier_from_caps_filename(in_caps_dwi)
# CAPS normalized FA
rename_fa = Rename()
rename_fa.inputs.in_file = in_norm_fa
rename_fa.inputs.format_string = (
f"{bids_identifier}_space-MNI152Lin_res-1x1x1_FA.nii.gz")
out_caps_fa = rename_fa.run()
# CAPS normalized MD
rename_md = Rename()
rename_md.inputs.in_file = in_norm_md
rename_md.inputs.format_string = (
f"{bids_identifier}_space-MNI152Lin_res-1x1x1_MD.nii.gz")
out_caps_md = rename_md.run()
# CAPS normalized AD
rename_ad = Rename()
rename_ad.inputs.in_file = in_norm_ad
rename_ad.inputs.format_string = (
f"{bids_identifier}_space-MNI152Lin_res-1x1x1_AD.nii.gz")
out_caps_ad = rename_ad.run()
# CAPS normalized RD
rename_rd = Rename()
rename_rd.inputs.in_file = in_norm_rd
rename_rd.inputs.format_string = (
f"{bids_identifier}_space-MNI152Lin_res-1x1x1_RD.nii.gz")
out_caps_rd = rename_rd.run()
# CAPS B-spline transform
rename_b_spline = Rename()
rename_b_spline.inputs.in_file = in_b_spline_transform
rename_b_spline.inputs.format_string = (
f"{bids_identifier}_space-MNI152Lin_res-1x1x1_deformation.nii.gz")
out_caps_b_spline_transform = rename_b_spline.run()
# CAPS Affine matrix
rename_affine = Rename()
rename_affine.inputs.in_file = in_affine_matrix
rename_affine.inputs.format_string = (
f"{bids_identifier}_space-MNI152Lin_res-1x1x1_affine.mat")
out_caps_affine_matrix = rename_affine.run()
return (
out_caps_fa.outputs.out_file,
out_caps_md.outputs.out_file,
out_caps_ad.outputs.out_file,
out_caps_rd.outputs.out_file,
out_caps_b_spline_transform.outputs.out_file,
out_caps_affine_matrix.outputs.out_file,
)
def rename_into_caps(in_caps_dwi,
in_norm_fa, in_norm_md, in_norm_ad, in_norm_rd,
in_b_spline_transform, in_affine_matrix):
"""
Rename the outputs of the pipelines into CAPS format namely:
<source_file>_space-T1w_preproc[.nii.gz|bval|bvec]
Args:
Returns:
The different outputs in CAPS format
"""
from nipype.utils.filemanip import split_filename
from nipype.interfaces.utility import Rename
import os
from clinica.pipelines.dwi_processing_dti.dwi_processing_dti_utils import extract_bids_identifier_from_caps_filename
bids_identifier = extract_bids_identifier_from_caps_filename(in_caps_dwi)
# Extract base path from fname:
base_dir_norm_fa, _, _ = split_filename(in_norm_fa)
base_dir_norm_md, _, _ = split_filename(in_norm_md)
base_dir_norm_ad, _, _ = split_filename(in_norm_ad)
base_dir_norm_rd, _, _ = split_filename(in_norm_rd)
base_dir_b_spline_transform, _, _ = split_filename(in_b_spline_transform)
base_dir_affine_matrix, _, _ = split_filename(in_affine_matrix)
# Rename into CAPS FA:
rename_fa = Rename()
rename_fa.inputs.in_file = in_norm_fa
rename_fa.inputs.format_string = os.path.join(
base_dir_norm_fa,
bids_identifier + "_space-MNI152Lin_res-1x1x1_fa.nii.gz")
out_caps_fa = rename_fa.run()
# Rename into CAPS MD:
rename_md = Rename()
rename_md.inputs.in_file = in_norm_md
rename_md.inputs.format_string = os.path.join(
base_dir_norm_md,
bids_identifier + "_space-MNI152Lin_res-1x1x1_md.nii.gz")
out_caps_md = rename_md.run()
# Rename into CAPS AD:
rename_ad = Rename()
rename_ad.inputs.in_file = in_norm_ad
rename_ad.inputs.format_string = os.path.join(
base_dir_norm_ad,
bids_identifier + "_space-MNI152Lin_res-1x1x1_ad.nii.gz")
out_caps_ad = rename_ad.run()
# Rename into CAPS RD:
rename_rd = Rename()
rename_rd.inputs.in_file = in_norm_rd
rename_rd.inputs.format_string = os.path.join(
base_dir_norm_rd,
bids_identifier + "_space-MNI152Lin_res-1x1x1_rd.nii.gz")
out_caps_rd = rename_rd.run()
# Rename into CAPS B-spline transform:
rename_b_spline = Rename()
rename_b_spline.inputs.in_file = in_b_spline_transform
rename_b_spline.inputs.format_string = os.path.join(
base_dir_b_spline_transform,
bids_identifier + "_space-MNI152Lin_res-1x1x1_deformation.nii.gz")
out_caps_b_spline_transform = rename_b_spline.run()
# Rename into CAPS Affine Matrix:
rename_affine = Rename()
rename_affine.inputs.in_file = in_affine_matrix
rename_affine.inputs.format_string = os.path.join(
base_dir_affine_matrix,
bids_identifier + "_space-MNI152Lin_res-1x1x1_affine.mat")
out_caps_affine_matrix = rename_affine.run()
from clinica.utils.stream import cprint
cprint("Renamed files:")
cprint(out_caps_fa.outputs.out_file)
cprint(out_caps_md.outputs.out_file)
cprint(out_caps_ad.outputs.out_file)
cprint(out_caps_rd.outputs.out_file)
cprint(out_caps_b_spline_transform.outputs.out_file)
cprint(out_caps_affine_matrix.outputs.out_file)
return out_caps_fa.outputs.out_file, out_caps_md.outputs.out_file,\
out_caps_ad.outputs.out_file, out_caps_rd.outputs.out_file, \
out_caps_b_spline_transform.outputs.out_file, \
out_caps_affine_matrix.outputs.out_file
