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Merged
merged 25 commits into from
Apr 27, 2016
Merged

[ENH] added interface for dcm2niix #1435

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01e5792
added interface for dcm2niix
mgxd Apr 15, 2016
231e813
dcm2niix add
mgxd Apr 15, 2016
778dccf
added new dcm2niix flag
mgxd Apr 15, 2016
28e1e1a
Update CHANGES
mgxd Apr 15, 2016
8c21803
fixed test
mgxd Apr 19, 2016
a473e8b
test fix
mgxd Apr 19, 2016
26818ba
Merge https://github.com/mgxd/nipype
mgxd Apr 19, 2016
13e131f
Update dcm2nii.py
mgxd Apr 19, 2016
fff34ae
Update dcm2nii.py
mgxd Apr 19, 2016
24863c9
removed white lines
mgxd Apr 19, 2016
7fa0ce8
upstream merge
mgxd Apr 19, 2016
68a9e8f
CHANGES updated
mgxd Apr 19, 2016
2f4f46d
removed white line
mgxd Apr 19, 2016
d0ccfde
doc test fix
mgxd Apr 20, 2016
a2c8764
Merge https://github.com/mgxd/nipype
mgxd Apr 20, 2016
62ca473
Merge https://github.com/nipy/nipype
mgxd Apr 20, 2016
3603523
default outname and single file doc test
mgxd Apr 20, 2016
4def5b7
Merge https://github.com/nipy/nipype
mgxd Apr 20, 2016
d3d30f4
reverted doc test
mgxd Apr 20, 2016
d16e693
Merge https://github.com/nipy/nipype
mgxd Apr 21, 2016
c3c7cfb
fix: compatible without bids option
mgxd Apr 21, 2016
a67b26f
fix: single file doctest
mgxd Apr 22, 2016
252a6d6
enh: desc for all inputs
mgxd Apr 23, 2016
8619c30
Merge https://github.com/nipy/nipype
mgxd Apr 25, 2016
269ca84
fix: additional desc info
mgxd Apr 25, 2016
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1 change: 1 addition & 0 deletions CHANGES
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
Release 0.12.0-rc1 (April 20, 2016)
============

* ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
* FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
Expand Down
166 changes: 151 additions & 15 deletions nipype/interfaces/dcm2nii.py
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Expand Up @@ -23,21 +23,35 @@ class Dcm2niiInputSpec(CommandLineInputSpec):
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)
config_file = File(exists=True, argstr="-b %s", genfile=True)
collapse_folders = traits.Bool(True, argstr='-c', usedefault=True)
date_in_filename = traits.Bool(True, argstr='-d', usedefault=True)
events_in_filename = traits.Bool(True, argstr='-e', usedefault=True)
source_in_filename = traits.Bool(False, argstr='-f', usedefault=True)
gzip_output = traits.Bool(False, argstr='-g', usedefault=True)
id_in_filename = traits.Bool(False, argstr='-i', usedefault=True)
nii_output = traits.Bool(True, argstr='-n', usedefault=True)
output_dir = Directory(exists=True, argstr='-o %s', genfile=True)
protocol_in_filename = traits.Bool(True, argstr='-p', usedefault=True)
reorient = traits.Bool(argstr='-r')
spm_analyze = traits.Bool(argstr='-s', xor=['nii_output'])
convert_all_pars = traits.Bool(True, argstr='-v', usedefault=True)
reorient_and_crop = traits.Bool(False, argstr='-x', usedefault=True)
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):
Expand Down Expand Up @@ -185,3 +199,125 @@ def _gen_filename(self, name):
f.close()
return config_file
return None


class Dcm2niixInputSpec(CommandLineInputSpec):
source_names = InputMultiPath(File(exists=True), argstr="%s", position=-1,
copyfile=False, mandatory=True, xor=['source_dir'])
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desc missing for all inputs.

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i know dcm2nii didn't have any either. but that should be fixed as well.

source_dir = Directory(exists=True, argstr="%s", position=-1, mandatory=True,
xor=['source_names'])
out_filename = traits.Str('%t%p', argstr="-f %s", usedefault=True,
desc="Output filename")
output_dir = Directory(exists=True, argstr='-o %s', genfile=True,
desc="Output directory")
bids_format = traits.Bool(True, argstr='-b', usedefault=True,
desc="Create a BIDS sidecar file")
compress = traits.Enum('i', ['y','i','n'], argstr='-z %s', usedefault=True,
desc="Gzip compress images - [y=pigz, i=internal, n=no]")
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="Convert only one image (filename as last input")
verbose = traits.Bool(False, argstr='-v', usedefault=True,
desc="Verbose output")


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_names = ['functional_1.dcm', 'functional_2.dcm']
>>> converter.inputs.compress = 'i'
>>> converter.inputs.single_file = True
>>> converter.inputs.output_dir = '.'
>>> converter.cmdline
'dcm2niix -b y -z i -m n -f %t%p -o . -s y -v n functional_1.dcm'
"""

input_spec = Dcm2niixInputSpec
output_spec = Dcm2niixOutputSpec
_cmd = 'dcm2niix'

def _format_arg(self, opt, spec, val):
if opt in ['bids_format', 'merge_imgs', 'single_file', 'verbose']:
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(Dcm2niix, self)._format_arg(opt, spec, val)

def _run_interface(self, runtime):
new_runtime = super(Dcm2niix, self)._run_interface(runtime)
if self.inputs.bids_format:
(self.output_files, self.bvecs,
self.bvals, self.bids) = self._parse_stdout(new_runtime.stdout)
else:
(self.output_files, self.bvecs,
self.bvals) = self._parse_stdout(new_runtime.stdout)
return new_runtime

def _parse_stdout(self, stdout):
files = []
bvecs = []
bvals = []
bids = []
skip = False
find_b = False
for line in stdout.split("\n"):
if not skip:
out_file = None
if line.startswith("Convert "): # output
fname = str(re.search('\S+/\S+', line).group(0))
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))
# extract bvals
if find_b:
bvecs.append(out_file + ".bvec")
bvals.append(out_file + ".bval")
find_b = False
# next scan will have bvals/bvecs
elif 'DTI gradient directions' in line:
find_b = True
else:
pass
if out_file:
files.append(out_file + ".nii.gz")
if self.inputs.bids_format:
bids.append(out_file + ".bids")
continue
skip = False
# just return what was done
if not bids:
return files, bvecs, bvals
else:
return files, bvecs, bvals, bids

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['converted_files'] = self.output_files
outputs['bvecs'] = self.bvecs
outputs['bvals'] = self.bvals
if self.inputs.bids_format:
outputs['bids'] = self.bids
return outputs

def _gen_filename(self, name):
if name == 'output_dir':
return os.getcwd()
return None