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dcm2nii.py
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dcm2nii.py
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# -*- coding: utf-8 -*-
"""dcm2nii converts images from the proprietary scanner DICOM format to NIfTI."""
import os
import re
from copy import deepcopy
import itertools as it
from glob import iglob
from ..utils.filemanip import split_filename
from .base import (
CommandLine,
CommandLineInputSpec,
InputMultiPath,
traits,
TraitedSpec,
OutputMultiPath,
isdefined,
File,
Directory,
PackageInfo,
)
class Info(PackageInfo):
"""Handle dcm2niix version information"""
version_cmd = "dcm2niix"
@staticmethod
def parse_version(raw_info):
m = re.search(r"version (\S+)", raw_info)
return m.groups()[0] if m else None
class Dcm2niiInputSpec(CommandLineInputSpec):
source_names = InputMultiPath(
File(exists=True),
argstr="%s",
position=-1,
copyfile=False,
mandatory=True,
xor=["source_dir"],
)
source_dir = Directory(
exists=True, argstr="%s", position=-1, mandatory=True, xor=["source_names"]
)
anonymize = traits.Bool(
True, argstr="-a", usedefault=True, desc="Remove identifying information"
)
config_file = File(
exists=True,
argstr="-b %s",
genfile=True,
desc="Load settings from specified inifile",
)
collapse_folders = traits.Bool(
True, argstr="-c", usedefault=True, desc="Collapse input folders"
)
date_in_filename = traits.Bool(
True, argstr="-d", usedefault=True, desc="Date in filename"
)
events_in_filename = traits.Bool(
True, argstr="-e", usedefault=True, desc="Events (series/acq) in filename"
)
source_in_filename = traits.Bool(
False, argstr="-f", usedefault=True, desc="Source filename"
)
gzip_output = traits.Bool(
False, argstr="-g", usedefault=True, desc="Gzip output (.gz)"
)
id_in_filename = traits.Bool(
False, argstr="-i", usedefault=True, desc="ID in filename"
)
nii_output = traits.Bool(
True,
argstr="-n",
usedefault=True,
desc="Save as .nii - if no, create .hdr/.img pair",
)
output_dir = Directory(
exists=True,
argstr="-o %s",
genfile=True,
desc="Output dir - if unspecified, source directory is used",
)
protocol_in_filename = traits.Bool(
True, argstr="-p", usedefault=True, desc="Protocol in filename"
)
reorient = traits.Bool(argstr="-r", desc="Reorient image to nearest orthogonal")
spm_analyze = traits.Bool(
argstr="-s", xor=["nii_output"], desc="SPM2/Analyze not SPM5/NIfTI"
)
convert_all_pars = traits.Bool(
True, argstr="-v", usedefault=True, desc="Convert every image in directory"
)
reorient_and_crop = traits.Bool(
False, argstr="-x", usedefault=True, desc="Reorient and crop 3D images"
)
class Dcm2niiOutputSpec(TraitedSpec):
converted_files = OutputMultiPath(File(exists=True))
reoriented_files = OutputMultiPath(File(exists=True))
reoriented_and_cropped_files = OutputMultiPath(File(exists=True))
bvecs = OutputMultiPath(File(exists=True))
bvals = OutputMultiPath(File(exists=True))
class Dcm2nii(CommandLine):
"""Uses MRIcron's dcm2nii to convert dicom files
Examples
========
>>> from nipype.interfaces.dcm2nii import Dcm2nii
>>> converter = Dcm2nii()
>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.gzip_output = True
>>> converter.inputs.output_dir = '.'
>>> converter.cmdline # doctest: +ELLIPSIS
'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
"""
input_spec = Dcm2niiInputSpec
output_spec = Dcm2niiOutputSpec
_cmd = "dcm2nii"
def _format_arg(self, opt, spec, val):
if opt in [
"anonymize",
"collapse_folders",
"date_in_filename",
"events_in_filename",
"source_in_filename",
"gzip_output",
"id_in_filename",
"nii_output",
"protocol_in_filename",
"reorient",
"spm_analyze",
"convert_all_pars",
"reorient_and_crop",
]:
spec = deepcopy(spec)
if val:
spec.argstr += " y"
else:
spec.argstr += " n"
val = True
if opt == "source_names":
return spec.argstr % val[0]
return super(Dcm2nii, self)._format_arg(opt, spec, val)
def _run_interface(self, runtime):
self._config_created = False
new_runtime = super(Dcm2nii, self)._run_interface(runtime)
(
self.output_files,
self.reoriented_files,
self.reoriented_and_cropped_files,
self.bvecs,
self.bvals,
) = self._parse_stdout(new_runtime.stdout)
if self._config_created:
os.remove("config.ini")
return new_runtime
def _parse_stdout(self, stdout):
files = []
reoriented_files = []
reoriented_and_cropped_files = []
bvecs = []
bvals = []
skip = False
last_added_file = None
for line in stdout.split("\n"):
if not skip:
out_file = None
if line.startswith("Saving "):
out_file = line[len("Saving ") :]
elif line.startswith("GZip..."):
# for gzipped output files are not absolute
fname = line[len("GZip...") :]
if len(files) and os.path.basename(files[-1]) == fname[:-3]:
# we are seeing a previously reported conversion
# as being saved in gzipped form -- remove the
# obsolete, uncompressed file
files.pop()
if isdefined(self.inputs.output_dir):
output_dir = self.inputs.output_dir
else:
output_dir = self._gen_filename("output_dir")
out_file = os.path.abspath(os.path.join(output_dir, fname))
elif line.startswith("Number of diffusion directions "):
if last_added_file:
base, filename, ext = split_filename(last_added_file)
bvecs.append(os.path.join(base, filename + ".bvec"))
bvals.append(os.path.join(base, filename + ".bval"))
elif line.startswith("Removed DWI from DTI scan"):
# such line can only follow the 'diffusion' case handled
# just above
for l in (bvecs, bvals):
l[-1] = os.path.join(
os.path.dirname(l[-1]), "x%s" % (os.path.basename(l[-1]),)
)
elif re.search(".*->(.*)", line):
val = re.search(".*->(.*)", line)
val = val.groups()[0]
if isdefined(self.inputs.output_dir):
output_dir = self.inputs.output_dir
else:
output_dir = self._gen_filename("output_dir")
val = os.path.join(output_dir, val)
if os.path.exists(val):
out_file = val
if out_file:
if out_file not in files:
files.append(out_file)
last_added_file = out_file
continue
if line.startswith("Reorienting as "):
reoriented_files.append(line[len("Reorienting as ") :])
skip = True
continue
elif line.startswith("Cropping NIfTI/Analyze image "):
base, filename = os.path.split(
line[len("Cropping NIfTI/Analyze image ") :]
)
filename = "c" + filename
if (
os.path.exists(os.path.join(base, filename))
or self.inputs.reorient_and_crop
):
# if reorient&crop is true but the file doesn't exist, this errors when setting outputs
reoriented_and_cropped_files.append(
os.path.join(base, filename)
)
skip = True
continue
skip = False
return files, reoriented_files, reoriented_and_cropped_files, bvecs, bvals
def _list_outputs(self):
outputs = self.output_spec().get()
outputs["converted_files"] = self.output_files
outputs["reoriented_files"] = self.reoriented_files
outputs["reoriented_and_cropped_files"] = self.reoriented_and_cropped_files
outputs["bvecs"] = self.bvecs
outputs["bvals"] = self.bvals
return outputs
def _gen_filename(self, name):
if name == "output_dir":
return os.getcwd()
elif name == "config_file":
self._config_created = True
config_file = "config.ini"
with open(config_file, "w") as f:
# disable interactive mode
f.write("[BOOL]\nManualNIfTIConv=0\n")
return config_file
return None
class Dcm2niixInputSpec(CommandLineInputSpec):
source_names = InputMultiPath(
File(exists=True),
argstr="%s",
position=-1,
copyfile=False,
mandatory=True,
desc=(
"A set of filenames to be converted. Note that the current "
"version (1.0.20180328) of dcm2niix converts any files in the "
"directory. To only convert specific files they should be in an "
"isolated directory"
),
xor=["source_dir"],
)
source_dir = Directory(
exists=True,
argstr="%s",
position=-1,
mandatory=True,
desc="A directory containing dicom files to be converted",
xor=["source_names"],
)
out_filename = traits.Str(
argstr="-f %s",
desc="Output filename template ("
"%a=antenna (coil) number, "
"%c=comments, "
"%d=description, "
"%e=echo number, "
"%f=folder name, "
"%i=ID of patient, "
"%j=seriesInstanceUID, "
"%k=studyInstanceUID, "
"%m=manufacturer, "
"%n=name of patient, "
"%p=protocol, "
"%s=series number, "
"%t=time, "
"%u=acquisition number, "
"%v=vendor, "
"%x=study ID; "
"%z=sequence name)",
)
output_dir = Directory(
".", usedefault=True, exists=True, argstr="-o %s", desc="Output directory"
)
bids_format = traits.Bool(
True, argstr="-b", usedefault=True, desc="Create a BIDS sidecar file"
)
anon_bids = traits.Bool(
argstr="-ba", requires=["bids_format"], desc="Anonymize BIDS"
)
compress = traits.Enum(
"y",
"i",
"n",
"3",
argstr="-z %s",
usedefault=True,
desc="Gzip compress images - [y=pigz, i=internal, n=no, 3=no,3D]",
)
merge_imgs = traits.Bool(
False, argstr="-m", usedefault=True, desc="merge 2D slices from same series"
)
single_file = traits.Bool(
False, argstr="-s", usedefault=True, desc="Single file mode"
)
verbose = traits.Bool(False, argstr="-v", usedefault=True, desc="Verbose output")
crop = traits.Bool(
False, argstr="-x", usedefault=True, desc="Crop 3D T1 acquisitions"
)
has_private = traits.Bool(
False,
argstr="-t",
usedefault=True,
desc="Text notes including private patient details",
)
compression = traits.Enum(
1,
2,
3,
4,
5,
6,
7,
8,
9,
argstr="-%d",
desc="Gz compression level (1=fastest, 9=smallest)",
)
comment = traits.Str(argstr="-c %s", desc="Comment stored as NIfTI aux_file")
ignore_deriv = traits.Bool(
argstr="-i", desc="Ignore derived, localizer and 2D images"
)
series_numbers = InputMultiPath(
traits.Str(),
argstr="-n %s...",
desc="Selectively convert by series number - can be used up to 16 times",
)
philips_float = traits.Bool(
argstr="-p", desc="Philips precise float (not display) scaling"
)
to_nrrd = traits.Bool(argstr="-e", desc="Export as NRRD instead of NIfTI")
class Dcm2niixOutputSpec(TraitedSpec):
converted_files = OutputMultiPath(File(exists=True))
bvecs = OutputMultiPath(File(exists=True))
bvals = OutputMultiPath(File(exists=True))
bids = OutputMultiPath(File(exists=True))
class Dcm2niix(CommandLine):
"""Uses Chris Rorden's dcm2niix to convert dicom files
Examples
========
>>> from nipype.interfaces.dcm2nii import Dcm2niix
>>> converter = Dcm2niix()
>>> converter.inputs.source_dir = 'dicomdir'
>>> converter.inputs.compression = 5
>>> converter.inputs.output_dir = 'ds005'
>>> converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n dicomdir'
>>> converter.run() # doctest: +SKIP
In the example below, we note that the current version of dcm2niix
converts any files in the directory containing the files in the list. We
also do not support nested filenames with this option. **Thus all files
must have a common root directory.**
>>> converter = Dcm2niix()
>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.compression = 5
>>> converter.inputs.output_dir = 'ds005'
>>> converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n .'
>>> converter.run() # doctest: +SKIP
"""
input_spec = Dcm2niixInputSpec
output_spec = Dcm2niixOutputSpec
_cmd = "dcm2niix"
@property
def version(self):
return Info.version()
def _format_arg(self, opt, spec, val):
bools = [
"bids_format",
"merge_imgs",
"single_file",
"verbose",
"crop",
"has_private",
"anon_bids",
"ignore_deriv",
"philips_float",
"to_nrrd",
]
if opt in bools:
spec = deepcopy(spec)
if val:
spec.argstr += " y"
else:
spec.argstr += " n"
val = True
if opt == "source_names":
return spec.argstr % (os.path.dirname(val[0]) or ".")
return super(Dcm2niix, self)._format_arg(opt, spec, val)
def _run_interface(self, runtime):
# may use return code 1 despite conversion
runtime = super(Dcm2niix, self)._run_interface(
runtime, correct_return_codes=(0, 1,)
)
self._parse_files(self._parse_stdout(runtime.stdout))
return runtime
def _parse_stdout(self, stdout):
filenames = []
for line in stdout.split("\n"):
if line.startswith("Convert "): # output
fname = str(re.search(r"\S+/\S+", line).group(0))
filenames.append(os.path.abspath(fname))
return filenames
def _parse_files(self, filenames):
outfiles, bvals, bvecs, bids = [], [], [], []
outtypes = [".bval", ".bvec", ".json", ".txt"]
if self.inputs.to_nrrd:
outtypes += [".nrrd", ".nhdr", ".raw.gz"]
else:
outtypes += [".nii", ".nii.gz"]
for filename in filenames:
# search for relevant files, and sort accordingly
for fl in search_files(filename, outtypes):
if (
fl.endswith(".nii")
or fl.endswith(".gz")
or fl.endswith(".nrrd")
or fl.endswith(".nhdr")
):
outfiles.append(fl)
elif fl.endswith(".bval"):
bvals.append(fl)
elif fl.endswith(".bvec"):
bvecs.append(fl)
elif fl.endswith(".json") or fl.endswith(".txt"):
bids.append(fl)
self.output_files = outfiles
self.bvecs = bvecs
self.bvals = bvals
self.bids = bids
def _list_outputs(self):
outputs = self.output_spec().get()
outputs["converted_files"] = self.output_files
outputs["bvecs"] = self.bvecs
outputs["bvals"] = self.bvals
outputs["bids"] = self.bids
return outputs
# https://stackoverflow.com/a/4829130
def search_files(prefix, outtypes):
return it.chain.from_iterable(iglob(prefix + outtype) for outtype in outtypes)