def get_dicom_info(c):
"""Get the dicom information for each subject
"""
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
import nipype.interfaces.freesurfer as fs
import nipype.pipeline.engine as pe
subjnode = pe.Node(interface=util.IdentityInterface(fields=['subject_id']),
name='subjinfo')
if c.test_mode:
subjnode.iterables = ('subject_id', [c.subjects[0]])
else:
subjnode.iterables = ('subject_id', c.subjects)
infonode = pe.Node(interface=fs.ParseDICOMDir(sortbyrun=True,
summarize=True),
name='dicominfo')
datasink = pe.Node(interface=nio.DataSink(parameterization=False), name='datasink')
datasink.inputs.base_directory = c.sink_dir
infopipe = pe.Workflow(name='extractinfo')
infopipe.base_dir = os.path.join(c.working_dir,'workdir')
infopipe.connect([(subjnode, datasink,[('subject_id','container')]),
(subjnode, infonode,[(('subject_id', get_subjectdcmdir, os.path.join(c.base_dir,c.dicom_dir_template)),
'dicom_dir')]),
(infonode, datasink,[('dicom_info_file','@info')]),
])
#infopipe.config = {'execution' : {'stop_on_first_crash' : True}}
if c.run_using_plugin:
infopipe.run(plugin=c.plugin,plugin_args=c.plugin_args)
else:
infopipe.run()
def test_parsedicomdir():
input_map = dict(
args=dict(argstr='%s', ),
dicom_dir=dict(
mandatory=True,
argstr='--d %s',
),
dicom_info_file=dict(argstr='--o %s', ),
environ=dict(),
sortbyrun=dict(argstr='--sortbyrun', ),
subjects_dir=dict(),
summarize=dict(argstr='--summarize', ),
)
instance = freesurfer.ParseDICOMDir()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(instance.inputs.traits()[key],
metakey), value
dicom2nifti.terminal_output = 'file'
# store nifti files output
dicom2nifti.inputs.output_dir = experiment_dir + data_dir
# specify optional inputs
#dicom2nifti.inputs.file_mapping = [('nifti', '*.nii'), ('info', 'dicom.txt'), ('dti', '*dti.bv*')]
#dicom2nifti.inputs.out_type = 'nii'
#dicom2nifti.inputs.subject_dir_template = '%s'
#------------------------------------------------------------
# Node ParseDICOMDIR - creates a nicer nifti overview textfile
#------------------------------------------------------------
dcminfo = pe.Node(interface = fs.ParseDICOMDir(), name = 'dcminfo')
dcminfo.inputs.sortbyrun = True
dcminfo.inputs.summarize = True
dcminfo.inputs.dicom_info_file = 'nifti_overview.txt'
#------------------------------------------------------------
# Initiation of 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'
def pathfinder(subjectname, foldername):
import os