def dcm_to_nifti(dicom_dir, nifti_dir, split=True, tool_used='dcm2niix'):
for patient in os.listdir(dicom_dir):
path_dicom = os.path.join(dicom_dir, patient)
path_nifti = os.path.join(nifti_dir, patient)
# make subfolder for each patient
if not os.path.exists(path_nifti):
os.makedirs(path_nifti)
if split == False:
if tool_used == 'dcm2niix':
converter = Dcm2niix()
converter.inputs.source_dir = path_dicom
converter.inputs.compression = 5
converter.inputs.merge_imgs = True
converter.inputs.out_filename = '%d'
converter.inputs.output_dir = path_nifti
converter.run()
elif tool_used == 'dcm2nii':
converter = Dcm2nii()
converter.inputs.source_dir = path_dicom
converter.inputs.gzip_output = True
converter.inputs.output_dir = path_nifti
converter.run()
else:
raise Warning("tool used does not exist, please enter dcm2nii or dcm2niix")
else:
for s in os.listdir(path_dicom):
if tool_used == 'dcm2niix':
converter = Dcm2niix()
converter.inputs.source_dir = path_dicom + '/' + s
converter.inputs.compression = 5
converter.inputs.merge_imgs = True
converter.inputs.out_filename = 'x_%d'
converter.inputs.output_dir = path_nifti
converter.run()
elif tool_used == 'dcm2nii':
converter = Dcm2nii()
converter.inputs.source_dir = path_dicom + '/' + s
converter.inputs.gzip_output = True
converter.inputs.output_dir = path_nifti
converter.run()
else:
raise Warning("tool used does not exist, please enter dcm2nii or dcm2niix")
#dcm_to_nifti(dicom_split_dir, nifti_dir, True, 'dcm2nii')
#dcm_to_nifti(dicom_split_dir, nifti_dir, True, 'dcm2niix')
def test_Dcm2nii_inputs():
input_map = dict(
anonymize=dict(argstr="-a", usedefault=True),
args=dict(argstr="%s"),
collapse_folders=dict(argstr="-c", usedefault=True),
config_file=dict(argstr="-b %s", genfile=True),
convert_all_pars=dict(argstr="-v", usedefault=True),
date_in_filename=dict(argstr="-d", usedefault=True),
environ=dict(nohash=True, usedefault=True),
events_in_filename=dict(argstr="-e", usedefault=True),
gzip_output=dict(argstr="-g", usedefault=True),
id_in_filename=dict(argstr="-i", usedefault=True),
ignore_exception=dict(nohash=True, usedefault=True),
nii_output=dict(argstr="-n", usedefault=True),
output_dir=dict(argstr="-o %s", genfile=True),
protocol_in_filename=dict(argstr="-p", usedefault=True),
reorient=dict(argstr="-r"),
reorient_and_crop=dict(argstr="-x", usedefault=True),
source_dir=dict(argstr="%s", mandatory=True, position=-1, xor=["source_names"]),
source_in_filename=dict(argstr="-f", usedefault=True),
source_names=dict(argstr="%s", copyfile=False, mandatory=True, position=-1, xor=["source_dir"]),
spm_analyze=dict(argstr="-s", xor=["nii_output"]),
terminal_output=dict(mandatory=True, nohash=True),
)
inputs = Dcm2nii.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def make_and_upload_nifti(subject_name, subject_XNAT, scan_sequence):
subject_directory = os.path.join(DICOM_folder, i_subject)
dicom_directory = os.path.join(DICOM_folder, i_subject, scan_sequence)
converter = Dcm2nii()
converter.inputs.source_dir = dicom_directory
converter.inputs.gzip_output = True
converter.inputs.output_dir = subject_directory
converter.inputs.source_in_filename = False
converter.inputs.protocol_in_filename = False
converter.inputs.date_in_filename = False
converter.inputs.events_in_filename = False
converter.inputs.id_in_filename = True
converter.inputs.terminal_output = 'file'
convert_result = converter.run()
nifti_file = convert_result.outputs.converted_files
shutil.move(nifti_file,
os.path.join(subject_directory, scan_sequence + '.nii.gz'))
nifti_file = os.path.join(subject_directory, scan_sequence + '.nii.gz')
upload_nifti(subject_XNAT, scan_sequence, nifti_file, 'NIFTI',
'image.nii.gz')
return
def dcm2nii_converter(source_names=traits.Undefined):
""" Create a dcm2nii workflow.
It does:
- dcm2nii
Nipype Inputs
-------------
source_names: traits.File
path to the DICOM files or series folder.
Returns
-------
wf: nipype Workflow
Note
----
For more info: http://www.mit.edu/~satra/nipype-nightly/interfaces/generated/nipype.interfaces.dcm2nii.html
# TODO: an attach function for this node.
"""
dcm2nii = Dcm2nii()
dcm2nii.inputs.gzip_output = True
dcm2nii.inputs.output_dir = '.'
dcm2nii.inputs.terminal_output = 'file'
dcm2nii.inputs.source_names = source_names
return dcm2nii
def weird_convert_dti_dcm(in_dcm):
import os
import numpy as np
import re
subjid = re.search('R[0-9X]+', in_dcm).group()
year = re.search('_201[1234]', in_dcm).group()[1:]
visit_dict = {'2012': 1, '2013': 2, '2014': 3, '2011': 4}
visit = visit_dict[year]
scanid = re.search('S[0-9]+', in_dcm).group()
ton_dir = '/data1/cooked/TONf'
test_fn = os.path.join(ton_dir, subjid, 'visit_{}'.format(visit), 'DTI',
'_'.join([subjid, 'visit', str(visit), 'DTI',
scanid])) + '.bvals'
if os.path.exists(test_fn):
assert np.all(np.loadtxt(test_fn) != 0)
converter = Dcm2nii()
converter.inputs.source_names = in_dcm
converter.inputs.gzip_output = True
converter.inputs.output_dir = os.getcwd()
converter.run()
merger = Merge()
merger.inputs.in_files = converter.output_files
merger.inputs.dimension = 't'
merged_result = merger.run()
fn_base = os.path.basename(in_dcm).split('.')[0]
merged_file = os.path.join(os.getcwd(), fn_base + '.nii.gz')
os.rename(merged_result.outputs.merged_file, merged_file)
in_bval = converter.bvals[0]
in_bvec = converter.bvecs[0]
b0_idx = 0
assert np.all(np.loadtxt(in_bval) != 0)
# Load (and transpose!!)
bvec_arr = np.loadtxt(in_bvec).T
out_bvec = np.zeros((bvec_arr.shape[0] + 1,
bvec_arr.shape[1]))
out_bvec[:] = np.nan
out_bvec[b0_idx, :] = 0
out_bvec[np.where(np.isnan(out_bvec))] = bvec_arr.flatten()
bval_arr = np.loadtxt(in_bval)
out_bval = np.zeros((bval_arr.shape[0] + 1,))
out_bval[:] = np.nan
out_bval[b0_idx] = 0
out_bval[np.isnan(out_bval)] = bval_arr
out_bvec_fn = os.path.join(os.getcwd(), fn_base + '.bvecs')
np.savetxt(out_bvec_fn, out_bvec, fmt='%.8f')
out_bval_fn = os.path.join(os.getcwd(), fn_base + '.bvals')
np.savetxt(out_bval_fn, out_bval, fmt='%.6f')
return merged_file, out_bvec_fn, out_bval_fn
def __init__(self, source_names=['path'], source_dir='path', **options):
from nipype.interfaces.dcm2nii import Dcm2nii
self.converter = Dcm2nii()
self.converter.inputs.source_names = source_names
self.converter.inputs.source_dir = source_dir
for ef in options:
setattr(self.converter.inputs, ef, options[ef])
self.converter.run()
def __init__(self, source_names=['', '']):
from nipype.interfaces.dcm2nii import Dcm2nii
converter = Dcm2nii()
converter.inputs.source_names = source_names
converter.inputs.gzip_output = True
converter.inputs.output_dir = '.'
converter.cmdline
converter.run()
def dcm_to_nifti(dicom_dir, nifti_dir, split=True, tool_used='dcm2niix'):
for patient in os.listdir(dicom_dir):
path_dicom = os.path.join(dicom_dir, patient)
path_nifti = os.path.join(nifti_dir, patient)
# make subfolder for each patient
if not os.path.exists(path_nifti):
os.makedirs(path_nifti)
if not split:
if tool_used == 'dcm2niix':
try:
subprocess.call('dcm2niix -z y -f %%d -o %s %s' %
(path_nifti, path_dicom),
shell=True)
except:
pass
elif tool_used == 'dcm2nii':
converter = Dcm2nii()
converter.inputs.source_dir = path_dicom
converter.inputs.gzip_output = True
converter.inputs.output_dir = path_nifti
converter.run()
else:
raise Warning(
"tool used does not exist, please enter dcm2nii or dcm2niix"
)
else:
for i in os.listdir(path_dicom):
if tool_used == 'dcm2niix':
try:
subprocess.call('dcm2niix -z y -f %%d -o %s %s' %
(path_nifti, path_dicom + '/' + i),
shell=True)
except:
pass
elif tool_used == 'dcm2nii':
converter = Dcm2nii()
converter.inputs.source_dir = path_dicom + '/' + i
converter.inputs.gzip_output = True
converter.inputs.output_dir = path_nifti
converter.run()
else:
raise Warning(
"tool used does not exist, please enter dcm2nii or dcm2niix"
)
def test_Dcm2nii_outputs():
output_map = dict(
bvals=dict(), bvecs=dict(), converted_files=dict(), reoriented_and_cropped_files=dict(), reoriented_files=dict()
)
outputs = Dcm2nii.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def create_converter_diffusion_pipeline(working_dir,
ds_dir,
name='converter_diffusion'):
# initiate workflow
converter_wf = Workflow(name=name)
converter_wf.base_dir = os.path.join(working_dir, 'LeiCA_resting')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['dMRI_dicom']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=['dMRI']),
name='outputnode')
niftisink = Node(nio.DataSink(), name='niftisink')
niftisink.inputs.base_directory = os.path.join(ds_dir, 'raw_niftis')
#######
converter_dMRI = Node(Dcm2nii(), name="converter_dMRI")
converter_dMRI.inputs.gzip_output = True
converter_dMRI.inputs.nii_output = True
converter_dMRI.inputs.anonymize = False
converter_dMRI.plugin_args = {'submit_specs': 'request_memory = 2000'}
converter_wf.connect(inputnode, 'dMRI_dicom', converter_dMRI,
'source_names')
dMRI_rename = Node(util.Rename(format_string='DTI_mx_137.nii.gz'),
name='dMRI_rename')
converter_wf.connect(converter_dMRI, 'converted_files', dMRI_rename,
'in_file')
bvecs_rename = Node(util.Rename(format_string='DTI_mx_137.bvecs'),
name='bvecs_rename')
converter_wf.connect(converter_dMRI, 'bvecs', bvecs_rename, 'in_file')
bvals_rename = Node(util.Rename(format_string='DTI_mx_137.bvals'),
name='bvals_rename')
converter_wf.connect(converter_dMRI, "bvals", bvals_rename, 'in_file')
# reorient to standard orientation
reor_2_std = Node(fsl.Reorient2Std(), name='reor_2_std')
converter_wf.connect(dMRI_rename, 'out_file', reor_2_std, 'in_file')
converter_wf.connect(reor_2_std, 'out_file', outputnode, 'dMRI')
# save original niftis
converter_wf.connect(reor_2_std, 'out_file', niftisink, 'dMRI.@dwi')
converter_wf.connect(bvals_rename, 'out_file', niftisink, 'dMRI.@bvals')
converter_wf.connect(bvecs_rename, 'out_file', niftisink, 'dMRI.@bvecs')
converter_wf.write_graph(dotfilename='converter_struct',
graph2use='flat',
format='pdf')
return converter_wf
def test_Dcm2nii_inputs():
input_map = dict(anonymize=dict(argstr='-a',
position=2,
),
args=dict(argstr='%s',
position=9,
),
config_file=dict(argstr='-b %s',
genfile=True,
position=7,
),
convert_all_pars=dict(argstr='-v',
position=8,
),
environ=dict(nohash=True,
usedefault=True,
),
gzip_output=dict(argstr='-g',
position=0,
usedefault=True,
),
id_in_filename=dict(argstr='-i',
position=3,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
nii_output=dict(argstr='-n',
position=1,
usedefault=True,
),
output_dir=dict(argstr='-o %s',
genfile=True,
position=6,
),
reorient=dict(argstr='-r',
position=4,
),
reorient_and_crop=dict(argstr='-x',
position=5,
),
source_names=dict(argstr='%s',
copyfile=False,
mandatory=True,
position=10,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
)
inputs = Dcm2nii.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def dcm_to_nifti(dicom_dir, nifti_dir, split=True, tool_used='dcm2niix'):
for patient in os.listdir(dicom_dir):
path_dicom = os.path.join(dicom_dir, patient)
path_nifti = os.path.join(nifti_dir, patient)
# make subfolder for each patient
if not os.path.exists(path_nifti):
os.makedirs(path_nifti)
if not split:
if tool_used == 'dcm2niix':
converter = Dcm2niix()
converter.inputs.source_dir = path_dicom
converter.inputs.compression = 5
converter.inputs.merge_imgs = True
converter.inputs.out_filename = '%d'
converter.inputs.output_dir = path_nifti
converter.run()
elif tool_used == 'dcm2nii':
converter = Dcm2nii()
converter.inputs.source_dir = path_dicom
converter.inputs.gzip_output = True
converter.inputs.output_dir = path_nifti
converter.run()
else:
raise Warning("tool used does not exist, please enter dcm2nii or dcm2niix")
else:
for s in os.listdir(path_dicom):
if tool_used == 'dcm2niix':
try:
subprocess.call('/home/harryzhang/toolbox/dcm2niix/console/dcm2niix -m y -5 -f %%d -o %s %s' %
(path_nifti, path_dicom + '/'+s), shell=True)
except:
pass
elif tool_used == 'dcm2nii':
converter = Dcm2nii()
converter.inputs.source_dir = path_dicom + '/' + s
converter.inputs.gzip_output = True
converter.inputs.output_dir = path_nifti
converter.run()
else:
raise Warning("tool used does not exist, please enter dcm2nii or dcm2niix")
def dcm2nii_wrapper(input_dir, output_dir):
converter = Dcm2nii()
converter.inputs.source_dir = input_dir
converter.inputs.output_dir = output_dir
converter.inputs.gzip_output = False
converter.inputs.reorient_and_crop = False
converter.inputs.reorient = False
converter.inputs.events_in_filename = False
converter.inputs.date_in_filename = False
converter.inputs.protocol_in_filename = True
converter.run()
return converter.output_files
def test_Dcm2nii_outputs():
output_map = dict(bvals=dict(),
bvecs=dict(),
converted_files=dict(),
reoriented_and_cropped_files=dict(),
reoriented_files=dict(),
)
outputs = Dcm2nii.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def main(args):
print('\n>> CLI Parameters ...\n')
print(args)
if not os.path.isdir(args.output_dir):
os.makedirs(args.output_dir)
converter = Dcm2nii()
converter.inputs.source_dir = args.source_dir
converter.inputs.output_dir = args.output_dir
converter.inputs.anonymize = args.anonymize
converter.inputs.nii_output = args.nii_output
converter.inputs.gzip_output = args.gzip_output
print('\n>> Running Dcm2nii ... \n')
print(converter.cmdline)
converter.run()
def extract_nac_pet(dicom_folder):
"""
Extract the Non attenuation Corrected PET from a DICOM exam.
The function extract the last frame of the DICOM exam.
The DICOM exam is expected to be of the dynamic PET scan itself. It also expects the image dimension
in the transversal acquisition direction to be of 127
It uses dcm2nii to convert the DICOM subset into a nifti file
:param dicom_folder: The input DICOM folder of the dynamic PET scan
:return: the nifti converted image file (the last frame of the dynamic PET scan)
"""
from glob import glob
import os
import shutil
import re
from nipype.interfaces.dcm2nii import Dcm2nii
def atoi(text):
return int(text) if text.isdigit() else text
def natural_keys(text):
return [atoi(c) for c in re.split('(\d+)', text)]
files = glob(os.path.join(os.path.abspath(dicom_folder), '*'))
sorted_files = sorted(files, key=natural_keys)
nac_pet_files = sorted_files[-127:]
for f in nac_pet_files:
shutil.copy(f, os.getcwd())
dcm2nii = Dcm2nii()
dcm2nii.inputs.source_dir = os.getcwd()
nii_outputs = dcm2nii.run().outputs.converted_files
print(nii_outputs)
return nii_outputs[0]
for subject in subjects_data_list:
if not os.path.exists(experiment_dir + '/' + data_dir_name + '/' +
subject):
os.makedirs(experiment_dir + '/' + data_dir_name + '/' + subject)
"""
Define nodes to use
"""
#Node: Infosource - we use IdentityInterface to create our own node, to
# specify the list of subjects the pipeline should be
# executed on
infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']),
name="infosource")
infosource.iterables = [('subject_id', subjects_data_list)]
dcm2nii_converter = pe.Node(interface=Dcm2nii(), name='dcm2nii')
dcm2nii_converter.inputs.gzip_output = True
dcm2nii_converter.inputs.reorient_and_crop = False
# Initiation of the preparation pipeline
prepareflow = pe.Workflow(name="prepareflow")
# Define where the workingdir of the all_consuming_workflow should be stored
# at
prepareflow.base_dir = experiment_dir + '/workingdir_prepareflow'
#Define pathfinder function
def pathfinder(subject, experiment_dir, foldername):
import os
from glob import glob
# Build DICOM scourse Direciry
def sourceFinder(subjectname):
import os
path_to_subject = '/Users/Dalton/Documents/FSL/ValuePilot/RawData'
path_to_dicomdir = 'DICOMDIR'
return os.path.join(path_to_subject, subjectname, path_to_dicomdir)
def outputFinder(subjectname):
import os
path_to_subject = '/Users/Dalton/Documents/FSL/ValuePilot/RawData'
path_to_dicomdir = 'niis'
return os.path.join(path_to_subject, subjectname, path_to_dicomdir)
converter = pe.Node(Dcm2nii(), name="converter")
converter.inputs.args = "-d n"
#Initiation of the preparation pipeline
prepareflow = pe.Workflow(name="prepareflow")
#Define where the workingdir of the all_consuming_workflow should be stored at
prepareflow.base_dir = experiment_dir + '/workingdir_prepareflow'
prepareflow.connect([(infosource, converter,
[(('subject_id', sourceFinder), 'source_names'),
(('subject_id', outputFinder), 'output_dir')])])
prepareflow.write_graph(graph2use='orig')
prepareflow.run(plugin='MultiProc', plugin_args={'n_procs': 8})
]]
datagrabber.inputs.template_args['1400'] = [[
'subject_id', 'session_1/RfMRI_mx_1400'
]]
datagrabber.inputs.template_args['2500'] = [[
'subject_id', 'session_1/RfMRI_std_2500'
]]
datagrabber.inputs.template_args['dwi'] = [[
'subject_id', ['session_1/DTI_mx_137/*.dcm']
]]
datagrabber.inputs.sort_filelist = True
datagrabber.inputs.raise_on_empty = False
wf.connect(subjects_infosource, "subject_id", datagrabber, "subject_id")
dcm2nii_dwi = pe.Node(Dcm2nii(), name="dcm2nii_dwi")
dcm2nii_dwi.inputs.gzip_output = True
dcm2nii_dwi.inputs.nii_output = True
dcm2nii_dwi.inputs.anonymize = False
dcm2nii_dwi.plugin_args = {'submit_specs': 'request_memory = 2000'}
wf.connect(datagrabber, "dwi", dcm2nii_dwi, "source_names")
dwi_rename = pe.Node(util.Rename(format_string="DTI_mx_137.nii.gz"),
name="dwi_rename")
wf.connect(dcm2nii_dwi, "converted_files", dwi_rename, "in_file")
bvecs_rename = pe.Node(util.Rename(format_string="DTI_mx_137.bvecs"),
name="bvecs_rename")
wf.connect(dcm2nii_dwi, "bvecs", bvecs_rename, "in_file")
bvals_rename = pe.Node(util.Rename(format_string="DTI_mx_137.bvals"),
def convert(items, anonymizer=None, symlink=True, converter=None):
prov_files = []
tmpdir = mkdtemp()
for item in items:
if isinstance(item[1], (list, tuple)):
outtypes = item[1]
else:
outtypes = [item[1]]
prefix = item[0]
print('Converting %s' % prefix)
dirname = os.path.dirname(prefix + '.ext')
print(dirname)
if not os.path.exists(dirname):
os.makedirs(dirname)
for outtype in outtypes:
print(outtype)
if outtype == 'dicom':
dicomdir = prefix + '_dicom'
if os.path.exists(dicomdir):
shutil.rmtree(dicomdir)
os.mkdir(dicomdir)
for filename in item[2]:
outfile = os.path.join(dicomdir, os.path.split(filename)[1])
if not os.path.islink(outfile):
if symlink:
os.symlink(filename, outfile)
else:
os.link(filename, outfile)
elif outtype in ['nii', 'nii.gz']:
outname = prefix + '.' + outtype
scaninfo = prefix + '_scaninfo.json'
if not os.path.exists(outname):
from nipype import config
config.enable_provenance()
from nipype import Function, Node
from nipype.interfaces.base import isdefined
print converter
if converter == 'mri_convert':
from nipype.interfaces.freesurfer.preprocess import MRIConvert
convertnode = Node(MRIConvert(), name = 'convert')
convertnode.base_dir = tmpdir
if outtype == 'nii.gz':
convertnode.inputs.out_type = 'niigz'
convertnode.inputs.in_file = item[2][0]
convertnode.inputs.out_file = outname
#cmd = 'mri_convert %s %s' % (item[2][0], outname)
#print(cmd)
#os.system(cmd)
res=convertnode.run()
elif converter == 'dcm2nii':
from nipype.interfaces.dcm2nii import Dcm2nii
convertnode = Node(Dcm2nii(), name='convert')
convertnode.base_dir = tmpdir
convertnode.inputs.source_names = item[2]
convertnode.inputs.gzip_output = outtype == 'nii.gz'
convertnode.inputs.terminal_output = 'allatonce'
res = convertnode.run()
if isinstance(res.outputs.converted_files, list):
print("Cannot convert dicom files - series likely has multiple orientations: ", item[2])
continue
else:
shutil.copyfile(res.outputs.converted_files, outname)
if isdefined(res.outputs.bvecs):
outname_bvecs = prefix + '.bvecs'
outname_bvals = prefix + '.bvals'
shutil.copyfile(res.outputs.bvecs, outname_bvecs)
shutil.copyfile(res.outputs.bvals, outname_bvals)
prov_file = prefix + '_prov.ttl'
shutil.copyfile(os.path.join(convertnode.base_dir,
convertnode.name,
'provenance.ttl'),
prov_file)
prov_files.append(prov_file)
embedfunc = Node(Function(input_names=['dcmfiles',
'niftifile',
'infofile',
'force'],
output_names=['outfile',
'meta'],
function=embed_nifti),
name='embedder')
embedfunc.inputs.dcmfiles = item[2]
embedfunc.inputs.niftifile = outname
embedfunc.inputs.infofile = scaninfo
embedfunc.inputs.force = True
embedfunc.base_dir = tmpdir
res = embedfunc.run()
g = res.provenance.rdf()
g.parse(prov_file,
format='turtle')
g.serialize(prov_file, format='turtle')
#out_file, meta_dict = embed_nifti(item[2], outname, force=True)
os.chmod(outname, 0440)
os.chmod(scaninfo, 0440)
os.chmod(prov_file, 0440)
shutil.rmtree(tmpdir)
## quick & basic converter for my own MRI files to swap into nifti from dicoms ## I deserve this for sitting in MRI scanner for an hour from nipype.interfaces.dcm2nii import Dcm2nii import networkx converter = Dcm2nii() # throw inputs here converter.inputs.source_names = ['./../ute/E5466S1I1.DCM'] # says this is a good idea online bc of size/compression converter.inputs.gzip_output = True converter.inputs.output_dir = '.' converter.cmdline '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 /../ute/E5466S1I1.DCM'
def Couple_Preproc_Pipeline(base_dir=None,
output_dir=None,
subject_id=None,
spm_path=None):
""" Create a preprocessing workflow for the Couples Conflict Study using nipype
Args:
base_dir: path to data folder where raw subject folder is located
output_dir: path to where key output files should be saved
subject_id: subject_id (str)
spm_path: path to spm folder
Returns:
workflow: a nipype workflow that can be run
"""
from nipype.interfaces.dcm2nii import Dcm2nii
from nipype.interfaces.fsl import Merge, TOPUP, ApplyTOPUP
import nipype.interfaces.io as nio
import nipype.interfaces.utility as util
from nipype.interfaces.utility import Merge as Merge_List
from nipype.pipeline.engine import Node, Workflow
from nipype.interfaces.fsl.maths import UnaryMaths
from nipype.interfaces.nipy.preprocess import Trim
from nipype.algorithms.rapidart import ArtifactDetect
from nipype.interfaces import spm
from nipype.interfaces.spm import Normalize12
from nipype.algorithms.misc import Gunzip
from nipype.interfaces.nipy.preprocess import ComputeMask
import nipype.interfaces.matlab as mlab
from nltools.utils import get_resource_path, get_vox_dims, get_n_volumes
from nltools.interfaces import Plot_Coregistration_Montage, PlotRealignmentParameters, Create_Covariates
import os
import glob
########################################
## Setup Paths and Nodes
########################################
# Specify Paths
canonical_file = os.path.join(spm_path, 'canonical', 'single_subj_T1.nii')
template_file = os.path.join(spm_path, 'tpm', 'TPM.nii')
# Set the way matlab should be called
mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")
mlab.MatlabCommand.set_default_paths(spm_path)
# Get File Names for different types of scans. Parse into separate processing streams
datasource = Node(interface=nio.DataGrabber(
infields=['subject_id'], outfields=['struct', 'ap', 'pa']),
name='datasource')
datasource.inputs.base_directory = base_dir
datasource.inputs.template = '*'
datasource.inputs.field_template = {
'struct': '%s/Study*/t1w_32ch_mpr_08mm*',
'ap': '%s/Study*/distortion_corr_32ch_ap*',
'pa': '%s/Study*/distortion_corr_32ch_pa*'
}
datasource.inputs.template_args = {
'struct': [['subject_id']],
'ap': [['subject_id']],
'pa': [['subject_id']]
}
datasource.inputs.subject_id = subject_id
datasource.inputs.sort_filelist = True
# iterate over functional scans to define paths
scan_file_list = glob.glob(
os.path.join(base_dir, subject_id, 'Study*', '*'))
func_list = [s for s in scan_file_list if "romcon_ap_32ch_mb8" in s]
func_list = [s for s in func_list
if "SBRef" not in s] # Exclude sbref for now.
func_source = Node(interface=util.IdentityInterface(fields=['scan']),
name="func_source")
func_source.iterables = ('scan', func_list)
# Create Separate Converter Nodes for each different type of file. (dist corr scans need to be done before functional)
ap_dcm2nii = Node(interface=Dcm2nii(), name='ap_dcm2nii')
ap_dcm2nii.inputs.gzip_output = True
ap_dcm2nii.inputs.output_dir = '.'
ap_dcm2nii.inputs.date_in_filename = False
pa_dcm2nii = Node(interface=Dcm2nii(), name='pa_dcm2nii')
pa_dcm2nii.inputs.gzip_output = True
pa_dcm2nii.inputs.output_dir = '.'
pa_dcm2nii.inputs.date_in_filename = False
f_dcm2nii = Node(interface=Dcm2nii(), name='f_dcm2nii')
f_dcm2nii.inputs.gzip_output = True
f_dcm2nii.inputs.output_dir = '.'
f_dcm2nii.inputs.date_in_filename = False
s_dcm2nii = Node(interface=Dcm2nii(), name='s_dcm2nii')
s_dcm2nii.inputs.gzip_output = True
s_dcm2nii.inputs.output_dir = '.'
s_dcm2nii.inputs.date_in_filename = False
########################################
## Setup Nodes for distortion correction
########################################
# merge output files into list
merge_to_file_list = Node(interface=Merge_List(2),
infields=['in1', 'in2'],
name='merge_to_file_list')
# fsl merge AP + PA files (depends on direction)
merger = Node(interface=Merge(dimension='t'), name='merger')
merger.inputs.output_type = 'NIFTI_GZ'
# use topup to create distortion correction map
topup = Node(interface=TOPUP(), name='topup')
topup.inputs.encoding_file = os.path.join(get_resource_path(),
'epi_params_APPA_MB8.txt')
topup.inputs.output_type = "NIFTI_GZ"
topup.inputs.config = 'b02b0.cnf'
# apply topup to all functional images
apply_topup = Node(interface=ApplyTOPUP(), name='apply_topup')
apply_topup.inputs.in_index = [1]
apply_topup.inputs.encoding_file = os.path.join(get_resource_path(),
'epi_params_APPA_MB8.txt')
apply_topup.inputs.output_type = "NIFTI_GZ"
apply_topup.inputs.method = 'jac'
apply_topup.inputs.interp = 'spline'
# Clear out Zeros from spline interpolation using absolute value.
abs_maths = Node(interface=UnaryMaths(), name='abs_maths')
abs_maths.inputs.operation = 'abs'
########################################
## Preprocessing
########################################
# Trim - remove first 10 TRs
n_vols = 10
trim = Node(interface=Trim(), name='trim')
trim.inputs.begin_index = n_vols
#Realignment - 6 parameters - realign to first image of very first series.
realign = Node(interface=spm.Realign(), name="realign")
realign.inputs.register_to_mean = True
#Coregister - 12 parameters
coregister = Node(interface=spm.Coregister(), name="coregister")
coregister.inputs.jobtype = 'estwrite'
#Plot Realignment
plot_realign = Node(interface=PlotRealignmentParameters(),
name="plot_realign")
#Artifact Detection
art = Node(interface=ArtifactDetect(), name="art")
art.inputs.use_differences = [True, False]
art.inputs.use_norm = True
art.inputs.norm_threshold = 1
art.inputs.zintensity_threshold = 3
art.inputs.mask_type = 'file'
art.inputs.parameter_source = 'SPM'
# Gunzip - unzip the functional and structural images
gunzip_struc = Node(Gunzip(), name="gunzip_struc")
gunzip_func = Node(Gunzip(), name="gunzip_func")
# Normalize - normalizes functional and structural images to the MNI template
normalize = Node(interface=Normalize12(jobtype='estwrite',
tpm=template_file),
name="normalize")
#Plot normalization Check
plot_normalization_check = Node(interface=Plot_Coregistration_Montage(),
name="plot_normalization_check")
plot_normalization_check.inputs.canonical_img = canonical_file
#Create Mask
compute_mask = Node(interface=ComputeMask(), name="compute_mask")
#remove lower 5% of histogram of mean image
compute_mask.inputs.m = .05
#Smooth
#implicit masking (.im) = 0, dtype = 0
smooth = Node(interface=spm.Smooth(), name="smooth")
smooth.inputs.fwhm = 6
#Create Covariate matrix
make_cov = Node(interface=Create_Covariates(), name="make_cov")
# Create a datasink to clean up output files
datasink = Node(interface=nio.DataSink(), name='datasink')
datasink.inputs.base_directory = output_dir
datasink.inputs.container = subject_id
########################################
# Create Workflow
########################################
workflow = Workflow(name='Preprocessed')
workflow.base_dir = os.path.join(base_dir, subject_id)
workflow.connect([
(datasource, ap_dcm2nii, [('ap', 'source_dir')]),
(datasource, pa_dcm2nii, [('pa', 'source_dir')]),
(datasource, s_dcm2nii, [('struct', 'source_dir')]),
(func_source, f_dcm2nii, [('scan', 'source_dir')]),
(ap_dcm2nii, merge_to_file_list, [('converted_files', 'in1')]),
(pa_dcm2nii, merge_to_file_list, [('converted_files', 'in2')]),
(merge_to_file_list, merger, [('out', 'in_files')]),
(merger, topup, [('merged_file', 'in_file')]),
(topup, apply_topup, [('out_fieldcoef', 'in_topup_fieldcoef'),
('out_movpar', 'in_topup_movpar')]),
(f_dcm2nii, trim, [('converted_files', 'in_file')]),
(trim, apply_topup, [('out_file', 'in_files')]),
(apply_topup, abs_maths, [('out_corrected', 'in_file')]),
(abs_maths, gunzip_func, [('out_file', 'in_file')]),
(gunzip_func, realign, [('out_file', 'in_files')]),
(s_dcm2nii, gunzip_struc, [('converted_files', 'in_file')]),
(gunzip_struc, coregister, [('out_file', 'source')]),
(coregister, normalize, [('coregistered_source', 'image_to_align')]),
(realign, coregister, [('mean_image', 'target'),
('realigned_files', 'apply_to_files')]),
(realign, normalize, [(('mean_image', get_vox_dims),
'write_voxel_sizes')]),
(coregister, normalize, [('coregistered_files', 'apply_to_files')]),
(normalize, smooth, [('normalized_files', 'in_files')]),
(realign, compute_mask, [('mean_image', 'mean_volume')]),
(compute_mask, art, [('brain_mask', 'mask_file')]),
(realign, art, [('realignment_parameters', 'realignment_parameters'),
('realigned_files', 'realigned_files')]),
(realign, plot_realign, [('realignment_parameters',
'realignment_parameters')]),
(normalize, plot_normalization_check, [('normalized_files', 'wra_img')
]),
(realign, make_cov, [('realignment_parameters',
'realignment_parameters')]),
(art, make_cov, [('outlier_files', 'spike_id')]),
(normalize, datasink, [('normalized_files', 'structural.@normalize')]),
(coregister, datasink, [('coregistered_source', 'structural.@struct')
]),
(topup, datasink, [('out_fieldcoef', 'distortion.@fieldcoef')]),
(topup, datasink, [('out_movpar', 'distortion.@movpar')]),
(smooth, datasink, [('smoothed_files', 'functional.@smooth')]),
(plot_realign, datasink, [('plot', 'functional.@plot_realign')]),
(plot_normalization_check, datasink,
[('plot', 'functional.@plot_normalization')]),
(make_cov, datasink, [('covariates', 'functional.@covariates')])
])
return workflow
def test_Dcm2nii_inputs():
input_map = dict(
anonymize=dict(
argstr='-a',
usedefault=True,
),
args=dict(argstr='%s', ),
collapse_folders=dict(
argstr='-c',
usedefault=True,
),
config_file=dict(
argstr='-b %s',
genfile=True,
),
convert_all_pars=dict(
argstr='-v',
usedefault=True,
),
date_in_filename=dict(
argstr='-d',
usedefault=True,
),
environ=dict(
nohash=True,
usedefault=True,
),
events_in_filename=dict(
argstr='-e',
usedefault=True,
),
gzip_output=dict(
argstr='-g',
usedefault=True,
),
id_in_filename=dict(
argstr='-i',
usedefault=True,
),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
nii_output=dict(
argstr='-n',
usedefault=True,
),
output_dir=dict(
argstr='-o %s',
genfile=True,
),
protocol_in_filename=dict(
argstr='-p',
usedefault=True,
),
reorient=dict(argstr='-r', ),
reorient_and_crop=dict(
argstr='-x',
usedefault=True,
),
source_dir=dict(
argstr='%s',
mandatory=True,
position=-1,
xor=['source_names'],
),
source_in_filename=dict(
argstr='-f',
usedefault=True,
),
source_names=dict(
argstr='%s',
copyfile=False,
mandatory=True,
position=-1,
xor=['source_dir'],
),
spm_analyze=dict(
argstr='-s',
xor=['nii_output'],
),
terminal_output=dict(
mandatory=True,
nohash=True,
),
)
inputs = Dcm2nii.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
### Grey Matter / White Matter post processing pipeline for T1/T2 weighted images ## based on commandline protocol from nipype.interfaces.dcm2nii import Dcm2nii import nipype.interfaces.fsl as fsl import nipype.pipeline.engine as pe import nipype.interfaces.io as nio converter = Dcm2nii() converter.inputs.source_names = ['E5466S1I1.DCM'] convert = pe.MapNode(interface=Dcm2nii(), name='conv', iterfield=['source_names']) # skull stripping bet = pe.MapNode(interface=fsl.BET(), name = 'bet', iterfield=['frac']) bet.inputs.frac = [0.8, 0.5, 0.2] # segmentation fast = pe.MapNode(interface=fsl.FAST(), name='fast', iterfield=['in_files']) # registration flirt = pe.MapNode(interface=fsl.FLIRT(), name='flirt', iterfield=['in_file']) ds = pe.Node(interface=nio.DataSink(), name="ds", iterfield=['in_files']) ds.inputs.base_directory = '.' workflow = pe.Workflow(name='T1_T2_Segmentation') workflow.base_dir = './output'
# <codecell>
from glob import glob
from nipype.interfaces.dcm2nii import Dcm2nii
from nipype.interfaces.fsl import DTIFit, BET
import nipype.pipeline.engine as pe
# <markdowncell>
# ### Version 2: Mapnodes
# <codecell>
convert = pe.MapNode(Dcm2nii(),
name='convert_dicom',
iterfield=['source_names'])
skull_stripper = pe.MapNode(BET(mask=True),
name='skull_stripper',
iterfield=['in_file'])
dtifit = pe.MapNode(DTIFit(),
name='dtifit',
iterfield=['dwi', 'bvals', 'bvecs', 'mask'])
convert_flow = pe.Workflow(name='convert_and_fit_mapnode')
convert_flow.connect([
(convert, dtifit, [('converted_files', 'dwi'), ('bvals', 'bvals'),
('bvecs', 'bvecs')]),
(convert, skull_stripper, [('converted_files', 'in_file')]),
(skull_stripper, dtifit, [('mask_file', 'mask')])
# Convert the T1 mgz image to nifti format for later usage
mriConverter = Node(freesurfer.preprocess.MRIConvert(),
name='convertAparcAseg')
#convertT1.inputs.out_file = subPath + reconallFolderName + '/mri/aparc+aseg.nii.gz'
mriConverter.inputs.out_type = 'niigz'
mriConverter.inputs.out_orientation = 'RAS'
# ### Diffusion Data (dwMRI) preprocessing
# In[ ]:
# First extract the diffusion vectors and the pulse intensity (bvec and bval)
# Use dcm2nii for this task
#dwiFinderNode = t1FinderNode.clone('dwiFinder')
dcm2niiNode = Node(Dcm2nii(), name='dcm2niiAndBvecs')
dcm2niiNode.inputs.gzip_output = True
dcm2niiNode.inputs.date_in_filename = False
dcm2niiNode.inputs.events_in_filename = False
# Extract the first image of the DTI series i.e. the b0 image
extrctB0Node = Node(Function(input_names=['dwMriFile'],
output_names=['b0'],
function=extractB0),
name='Extract_b0')
# Perform the registration between subject T1 space and dwMRI space
bbregNode = Node(freesurfer.preprocess.BBRegister(), name='BBRegister')
bbregNode.inputs.init = "fsl"
bbregNode.inputs.contrast_type = "t2"
bbregNode.inputs.epi_mask = True
def create_gif_pseudoct_workflow(in_ute_echo2_file,
in_ute_umap_dir,
in_db_file,
cpp_dir,
in_t1_file=None,
in_t2_file=None,
in_mask_file=None,
in_nac_pet_dir=None,
name='gif_pseudoct'):
"""create_niftyseg_gif_propagation_pipeline.
@param in_ute_echo2_file input UTE echo file
@param in_ute_umap_dir input UTE umap file
@param in_db_file input database xml file for the GIF algorithm
@param cpp_dir cpp directory
@param in_t1_file input T1 target file
@param in_t2_file input T2 target file
@param in_mask_file optional input mask for the target T1 file
@param name optional name of the pipeline
"""
in_file = in_t1_file if in_t1_file else in_t2_file
subject_id = split_filename(os.path.basename(in_file))[1]
workflow = pe.Workflow(name=name)
workflow.base_output_dir = name
gif = pe.Node(interface=Gif(database_file=in_db_file,
cpp_dir=cpp_dir,
lncc_ker=3,
regNMI=True,
regBE=0.01),
name='gif')
if in_mask_file:
gif.inputs.mask_file = in_mask_file
# Create empty masks for the bias correction to cover the full image
t1_full_mask = pe.Node(interface=niu.Function(input_names=['in_file'],
output_names=['out_file'],
function=create_full_mask),
name='t1_full_mask')
t1_full_mask.inputs.in_file = in_t1_file
t2_full_mask = pe.Node(interface=niu.Function(input_names=['in_file'],
output_names=['out_file'],
function=create_full_mask),
name='t2_full_mask')
t2_full_mask.inputs.in_file = in_t2_file
# Create bias correction nodes that are adapted to our needs. i.e. Boost the T2 bias correction
bias_correction_t1 = pe.Node(interface=N4BiasCorrection(),
name='bias_correction_t1')
if in_t1_file:
bias_correction_t1.inputs.in_file = in_t1_file
# Create bias correction nodes that are adapted to our needs. i.e. Boost the T2 bias correction
bias_correction_t2 = pe.Node(interface=N4BiasCorrection(
in_maxiter=300, in_convergence=0.0001),
name='bias_correction_t2')
if in_t2_file:
bias_correction_t2.inputs.in_file = in_t2_file
# Only connect the nodes if the input image exist respectively
if in_t1_file:
workflow.connect(t1_full_mask, 'out_file', bias_correction_t1,
'mask_file')
if in_t2_file:
workflow.connect(t2_full_mask, 'out_file', bias_correction_t2,
'mask_file')
if in_t1_file and in_t2_file:
affine_mr_target = pe.Node(interface=niftyreg.RegAladin(maxit_val=10),
name='affine_mr_target')
workflow.connect(bias_correction_t1, 'out_file', affine_mr_target,
'ref_file')
workflow.connect(bias_correction_t2, 'out_file', affine_mr_target,
'flo_file')
resample_mr_target = pe.Node(
interface=niftyreg.RegResample(pad_val=float('nan')),
name='resample_MR_target')
workflow.connect(bias_correction_t1, 'out_file', resample_mr_target,
'ref_file')
workflow.connect(bias_correction_t2, 'out_file', resample_mr_target,
'flo_file')
lister = pe.Node(interface=niu.Merge(2), name='lister')
merger = pe.Node(interface=fsl.Merge(dimension='t',
output_type='NIFTI_GZ'),
name='fsl_merge')
workflow.connect(affine_mr_target, 'aff_file', resample_mr_target,
'trans_file')
workflow.connect(bias_correction_t1, 'out_file', lister, 'in1')
workflow.connect(resample_mr_target, 'out_file', lister, 'in2')
workflow.connect(lister, 'out', merger, 'in_files')
workflow.connect(merger, 'merged_file', gif, 'in_file')
else:
if in_t1_file:
workflow.connect(bias_correction_t1, 'out_file', gif, 'in_file')
if in_t2_file:
workflow.connect(bias_correction_t2, 'out_file', gif, 'in_file')
pct_hu_to_umap = pe.Node(interface=niu.Function(
input_names=['pCT_file', 'structural_mri_file', 'ute_echo2_file'],
output_names=['pct_umap_file'],
function=convert_pct_hu_to_umap),
name='pCT_HU_to_umap')
pct_hu_to_umap.inputs.structural_mri_file = in_file
pct_hu_to_umap.inputs.ute_echo2_file = in_ute_echo2_file
workflow.connect(gif, 'synth_file', pct_hu_to_umap, 'pCT_file')
pct2dcm_pct_umap = pe.Node(interface=Pct2Dcm(in_umap_name='pCT_umap'),
name='pct2dcm_pct_umap')
workflow.connect(pct_hu_to_umap, 'pct_umap_file', pct2dcm_pct_umap,
'in_umap_file')
pct2dcm_pct_umap.inputs.in_ute_umap_dir = os.path.abspath(in_ute_umap_dir)
merger_output_number = 2
pct2dcm_ute_umap_end = None
pct2dcm_pct_umap_end = None
if in_nac_pet_dir:
ute_umap_dcm2nii = pe.Node(
interface=Dcm2nii(source_dir=in_ute_umap_dir),
name='ute_umap_dcm2nii')
first_item_selector = pe.Node(interface=niu.Select(index=0),
name='first_item_selector')
workflow.connect(ute_umap_dcm2nii, 'converted_files',
first_item_selector, 'inlist')
nac_extractor = pe.Node(interface=niu.Function(
input_names=['dicom_folder'],
output_names=['nifti_file'],
function=extract_nac_pet),
name='nac_extractor')
nac_extractor.inputs.dicom_folder = in_nac_pet_dir
ute_to_nac_registration = pe.Node(
interface=niftyreg.RegAladin(rig_only_flag=True),
name='ute_to_nac_registration')
workflow.connect(nac_extractor, 'nifti_file', ute_to_nac_registration,
'ref_file')
ute_to_nac_registration.inputs.flo_file = in_ute_echo2_file
ute_resample = pe.Node(interface=niftyreg.RegResample(),
name='ute_resample')
workflow.connect(first_item_selector, 'out', ute_resample, 'ref_file')
workflow.connect(first_item_selector, 'out', ute_resample, 'flo_file')
workflow.connect(ute_to_nac_registration, 'aff_file', ute_resample,
'aff_file')
pct2dcm_ute_umap_end = pe.Node(
interface=Pct2Dcm(in_umap_name='UTE_umap_end'),
name='pct2dcm_ute_umap_end')
workflow.connect(ute_resample, 'res_file', pct2dcm_ute_umap_end,
'in_umap_file')
pct2dcm_ute_umap_end.inputs.in_ute_umap_dir = os.path.abspath(
in_ute_umap_dir)
pct_resample = pe.Node(interface=niftyreg.RegResample(),
name='pct_resample')
workflow.connect(pct_hu_to_umap, 'pct_umap_file', pct_resample,
'ref_file')
workflow.connect(pct_hu_to_umap, 'pct_umap_file', pct_resample,
'flo_file')
workflow.connect(ute_to_nac_registration, 'aff_file', pct_resample,
'aff_file')
pct2dcm_pct_umap_end = pe.Node(
interface=Pct2Dcm(in_umap_name='pCT_umap_end'),
name='pct2dcm_pct_umap_end')
workflow.connect(pct_resample, 'res_file', pct2dcm_pct_umap_end,
'in_umap_file')
pct2dcm_pct_umap_end.inputs.in_ute_umap_dir = os.path.abspath(
in_ute_umap_dir)
merger_output_number = 4
# merge output
output_merger = pe.Node(
interface=niu.Merge(numinputs=merger_output_number),
name='output_merger')
workflow.connect(gif, 'synth_file', output_merger, 'in1')
workflow.connect(pct2dcm_pct_umap, 'output_file', output_merger, 'in2')
renamer = pe.Node(interface=niu.Rename(format_string=subject_id +
"_%(type)s",
keep_ext=True),
name='renamer')
if in_nac_pet_dir:
workflow.connect(pct2dcm_ute_umap_end, 'output_file', output_merger,
'in3')
workflow.connect(pct2dcm_pct_umap_end, 'output_file', output_merger,
'in4')
renamer.inputs.type = ['synth', 'pct', 'ute_end', 'pct_end']
else:
renamer.inputs.type = ['synth', 'pct']
workflow.connect(output_merger, 'out', renamer, 'in_file')
return workflow
def test_Dcm2nii_inputs():
input_map = dict(anonymize=dict(argstr='-a',
usedefault=True,
),
args=dict(argstr='%s',
),
collapse_folders=dict(argstr='-c',
usedefault=True,
),
config_file=dict(argstr='-b %s',
genfile=True,
),
convert_all_pars=dict(argstr='-v',
usedefault=True,
),
date_in_filename=dict(argstr='-d',
usedefault=True,
),
environ=dict(nohash=True,
usedefault=True,
),
events_in_filename=dict(argstr='-e',
usedefault=True,
),
gzip_output=dict(argstr='-g',
usedefault=True,
),
id_in_filename=dict(argstr='-i',
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
nii_output=dict(argstr='-n',
usedefault=True,
),
output_dir=dict(argstr='-o %s',
genfile=True,
),
protocol_in_filename=dict(argstr='-p',
usedefault=True,
),
reorient=dict(argstr='-r',
),
reorient_and_crop=dict(argstr='-x',
usedefault=True,
),
source_dir=dict(argstr='%s',
mandatory=True,
position=-1,
xor=['source_names'],
),
source_in_filename=dict(argstr='-f',
usedefault=True,
),
source_names=dict(argstr='%s',
copyfile=False,
mandatory=True,
position=-1,
xor=['source_dir'],
),
spm_analyze=dict(argstr='-s',
xor=['nii_output'],
),
terminal_output=dict(nohash=True,
),
)
inputs = Dcm2nii.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
