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satrasatra
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Merge pull request #1435 from mgxd/master
[ENH] added interface for dcm2niix
2 parents 34c3b8b + 269ca84 commit aeecd2f

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
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Release 0.12.0-rc1 (April 20, 2016)
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============
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* ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
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* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
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* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
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* FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)

‎nipype/interfaces/dcm2nii.py

Lines changed: 151 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -23,21 +23,35 @@ class Dcm2niiInputSpec(CommandLineInputSpec):
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copyfile=False, mandatory=True, xor=['source_dir'])
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source_dir = Directory(exists=True, argstr="%s", position=-1, mandatory=True,
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xor=['source_names'])
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anonymize = traits.Bool(True, argstr='-a', usedefault=True)
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config_file = File(exists=True, argstr="-b %s", genfile=True)
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collapse_folders = traits.Bool(True, argstr='-c', usedefault=True)
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date_in_filename = traits.Bool(True, argstr='-d', usedefault=True)
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events_in_filename = traits.Bool(True, argstr='-e', usedefault=True)
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source_in_filename = traits.Bool(False, argstr='-f', usedefault=True)
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gzip_output = traits.Bool(False, argstr='-g', usedefault=True)
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id_in_filename = traits.Bool(False, argstr='-i', usedefault=True)
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nii_output = traits.Bool(True, argstr='-n', usedefault=True)
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output_dir = Directory(exists=True, argstr='-o %s', genfile=True)
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protocol_in_filename = traits.Bool(True, argstr='-p', usedefault=True)
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reorient = traits.Bool(argstr='-r')
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spm_analyze = traits.Bool(argstr='-s', xor=['nii_output'])
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convert_all_pars = traits.Bool(True, argstr='-v', usedefault=True)
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reorient_and_crop = traits.Bool(False, argstr='-x', usedefault=True)
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anonymize = traits.Bool(True, argstr='-a', usedefault=True,
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desc="Remove identifying information")
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config_file = File(exists=True, argstr="-b %s", genfile=True,
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desc="Load settings from specified inifile")
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collapse_folders = traits.Bool(True, argstr='-c', usedefault=True,
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desc="Collapse input folders")
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date_in_filename = traits.Bool(True, argstr='-d', usedefault=True,
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desc="Date in filename")
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events_in_filename = traits.Bool(True, argstr='-e', usedefault=True,
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desc="Events (series/acq) in filename")
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source_in_filename = traits.Bool(False, argstr='-f', usedefault=True,
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desc="Source filename")
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gzip_output = traits.Bool(False, argstr='-g', usedefault=True,
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desc="Gzip output (.gz)")
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id_in_filename = traits.Bool(False, argstr='-i', usedefault=True,
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desc="ID in filename")
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nii_output = traits.Bool(True, argstr='-n', usedefault=True,
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desc="Save as .nii - if no, create .hdr/.img pair")
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output_dir = Directory(exists=True, argstr='-o %s', genfile=True,
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desc="Output dir - if unspecified, source directory is used")
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protocol_in_filename = traits.Bool(True, argstr='-p', usedefault=True,
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desc="Protocol in filename")
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reorient = traits.Bool(argstr='-r', desc="Reorient image to nearest orthogonal")
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spm_analyze = traits.Bool(argstr='-s', xor=['nii_output'],
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desc="SPM2/Analyze not SPM5/NIfTI")
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convert_all_pars = traits.Bool(True, argstr='-v', usedefault=True,
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desc="Convert every image in directory")
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reorient_and_crop = traits.Bool(False, argstr='-x', usedefault=True,
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desc="Reorient and crop 3D images")
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class Dcm2niiOutputSpec(TraitedSpec):
@@ -185,3 +199,125 @@ def _gen_filename(self, name):
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f.close()
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return config_file
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return None
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class Dcm2niixInputSpec(CommandLineInputSpec):
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source_names = InputMultiPath(File(exists=True), argstr="%s", position=-1,
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copyfile=False, mandatory=True, xor=['source_dir'])
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source_dir = Directory(exists=True, argstr="%s", position=-1, mandatory=True,
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xor=['source_names'])
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out_filename = traits.Str('%t%p', argstr="-f %s", usedefault=True,
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desc="Output filename")
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output_dir = Directory(exists=True, argstr='-o %s', genfile=True,
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desc="Output directory")
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bids_format = traits.Bool(True, argstr='-b', usedefault=True,
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desc="Create a BIDS sidecar file")
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compress = traits.Enum('i', ['y','i','n'], argstr='-z %s', usedefault=True,
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desc="Gzip compress images - [y=pigz, i=internal, n=no]")
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merge_imgs = traits.Bool(False, argstr='-m', usedefault=True,
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desc="merge 2D slices from same series")
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single_file = traits.Bool(False, argstr='-s', usedefault=True,
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desc="Convert only one image (filename as last input")
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verbose = traits.Bool(False, argstr='-v', usedefault=True,
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desc="Verbose output")
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class Dcm2niixOutputSpec(TraitedSpec):
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converted_files = OutputMultiPath(File(exists=True))
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bvecs = OutputMultiPath(File(exists=True))
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bvals = OutputMultiPath(File(exists=True))
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bids = OutputMultiPath(File(exists=True))
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class Dcm2niix(CommandLine):
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"""Uses Chris Rorden's dcm2niix to convert dicom files
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Examples
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========
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>>> from nipype.interfaces.dcm2nii import Dcm2niix
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>>> converter = Dcm2niix()
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>>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
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>>> converter.inputs.compress = 'i'
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>>> converter.inputs.single_file = True
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>>> converter.inputs.output_dir = '.'
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>>> converter.cmdline
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'dcm2niix -b y -z i -m n -f %t%p -o . -s y -v n functional_1.dcm'
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"""
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input_spec = Dcm2niixInputSpec
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output_spec = Dcm2niixOutputSpec
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_cmd = 'dcm2niix'
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def _format_arg(self, opt, spec, val):
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if opt in ['bids_format', 'merge_imgs', 'single_file', 'verbose']:
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spec = deepcopy(spec)
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if val:
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spec.argstr += ' y'
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else:
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spec.argstr += ' n'
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val = True
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if opt == 'source_names':
259+
return spec.argstr % val[0]
260+
return super(Dcm2niix, self)._format_arg(opt, spec, val)
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def _run_interface(self, runtime):
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new_runtime = super(Dcm2niix, self)._run_interface(runtime)
264+
if self.inputs.bids_format:
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(self.output_files, self.bvecs,
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self.bvals, self.bids) = self._parse_stdout(new_runtime.stdout)
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else:
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(self.output_files, self.bvecs,
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self.bvals) = self._parse_stdout(new_runtime.stdout)
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return new_runtime
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def _parse_stdout(self, stdout):
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files = []
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bvecs = []
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bvals = []
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bids = []
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skip = False
278+
find_b = False
279+
for line in stdout.split("\n"):
280+
if not skip:
281+
out_file = None
282+
if line.startswith("Convert "): # output
283+
fname = str(re.search('\S+/\S+', line).group(0))
284+
if isdefined(self.inputs.output_dir):
285+
output_dir = self.inputs.output_dir
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else:
287+
output_dir = self._gen_filename('output_dir')
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out_file = os.path.abspath(os.path.join(output_dir, fname))
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# extract bvals
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if find_b:
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bvecs.append(out_file + ".bvec")
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bvals.append(out_file + ".bval")
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find_b = False
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# next scan will have bvals/bvecs
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elif 'DTI gradient directions' in line:
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find_b = True
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else:
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pass
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if out_file:
300+
files.append(out_file + ".nii.gz")
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if self.inputs.bids_format:
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bids.append(out_file + ".bids")
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continue
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skip = False
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# just return what was done
306+
if not bids:
307+
return files, bvecs, bvals
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else:
309+
return files, bvecs, bvals, bids
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['converted_files'] = self.output_files
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outputs['bvecs'] = self.bvecs
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outputs['bvals'] = self.bvals
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if self.inputs.bids_format:
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outputs['bids'] = self.bids
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return outputs
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def _gen_filename(self, name):
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if name == 'output_dir':
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return os.getcwd()
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return None

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