def detect_inputs(t1w_list,
t2w_list=None,
flair_list=None,
hires_enabled=True):
t1w_list = filename_to_list(t1w_list)
t2w_list = filename_to_list(t2w_list) if t2w_list is not None else []
flair_list = filename_to_list(flair_list) if flair_list is not None else []
t1w_ref = nb.load(t1w_list[0])
# Use high resolution preprocessing if voxel size < 1.0mm
# Tolerance of 0.05mm requires that rounds down to 0.9mm or lower
hires = hires_enabled and max(t1w_ref.header.get_zooms()) < 1 - 0.05
t2w = None
if t2w_list and max(nb.load(t2w_list[0]).header.get_zooms()) < 1.2:
t2w = t2w_list[0]
# Prefer T2w to FLAIR if both present and T2w satisfies
flair = None
if flair_list and not t2w and max(
nb.load(flair_list[0]).header.get_zooms()) < 1.2:
flair = flair_list[0]
# https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon
mris_inflate = '-n 50' if hires else None
return (t2w, flair, hires, mris_inflate)
def detect_inputs(t1w_list, t2w_list=[], hires_enabled=True):
from niworkflows.nipype.interfaces.base import isdefined
from niworkflows.nipype.utils.filemanip import filename_to_list
from niworkflows.nipype.interfaces.traits_extension import Undefined
import nibabel as nib
t1w_list = filename_to_list(t1w_list)
t2w_list = filename_to_list(t2w_list) if isdefined(t2w_list) else []
t1w_ref = nib.load(t1w_list[0])
# Use high resolution preprocessing if voxel size < 1.0mm
# Tolerance of 0.05mm requires that rounds down to 0.9mm or lower
hires = hires_enabled and max(t1w_ref.header.get_zooms()) < 1 - 0.05
t2w = Undefined
if t2w_list and max(nib.load(t2w_list[0]).header.get_zooms()) < 1.2:
t2w = t2w_list[0]
# https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon
mris_inflate = '-n 50' if hires else Undefined
return (t2w, isdefined(t2w), hires, mris_inflate)
def add_suffix(in_files, suffix):
"""
Wrap nipype's fname_presuffix to conveniently just add a prefix
>>> add_suffix([
... '/path/to/sub-045_ses-test_T1w.nii.gz',
... '/path/to/sub-045_ses-retest_T1w.nii.gz'], '_test')
'sub-045_ses-test_T1w_test.nii.gz'
"""
import os.path as op
from niworkflows.nipype.utils.filemanip import fname_presuffix, filename_to_list
return op.basename(
fname_presuffix(filename_to_list(in_files)[0], suffix=suffix))
def fix_multi_T1w_source_name(in_files):
"""
Make up a generic source name when there are multiple T1s
>>> fix_multi_T1w_source_name([
... '/path/to/sub-045_ses-test_T1w.nii.gz',
... '/path/to/sub-045_ses-retest_T1w.nii.gz'])
'/path/to/sub-045_T1w.nii.gz'
"""
import os
from niworkflows.nipype.utils.filemanip import filename_to_list
base, in_file = os.path.split(filename_to_list(in_files)[0])
subject_label = in_file.split("_", 1)[0].split("-")[1]
return os.path.join(base, "sub-%s_T1w.nii.gz" % subject_label)
def _flatten(l):
from niworkflows.nipype.utils.filemanip import filename_to_list
return [item for sublist in l for item in filename_to_list(sublist)]
def add_suffix(in_files, suffix):
import os.path as op
from niworkflows.nipype.utils.filemanip import fname_presuffix, filename_to_list
return op.basename(
fname_presuffix(filename_to_list(in_files)[0], suffix=suffix))
def add_suffix(in_files, suffix):
import os.path as op
from niworkflows.nipype.utils.filemanip import fname_presuffix, filename_to_list
return op.basename(fname_presuffix(filename_to_list(in_files)[0],
suffix=suffix))
