Ejemplos de create_tbss_non_FA en Python

Ejemplo n.º 1

Archivo: dti_preproc.py Proyecto: shanqing-cai/BrainImagingPipelines

def create_tbss():
    """
    TBSS analysis
    """
    #tbss_source = get_tbss_source()
    inputnode = pe.Node(interface=util.IdentityInterface(fields=['fa_list','md_list']),
                        name='inputspec')
                        
    tbss_all = create_tbss_all()
    tbss_all.inputs.inputnode.skeleton_thresh = skeleton_thresh

    tbssproc = pe.Workflow(name="tbssproc")
    tbssproc.base_dir = os.path.join(os.path.abspath(workingdir), 'l2')
    
    tbssproc.connect(inputnode, 'fa_list', tbss_all, 'inputnode.fa_list')

    tbss_MD = create_tbss_non_FA(name='tbss_MD')
    tbss_MD.inputs.inputnode.skeleton_thresh = tbss_all.inputs.inputnode.skeleton_thresh

    tbssproc.connect([(tbss_all, tbss_MD, [('tbss2.outputnode.field_list',
                                            'inputnode.field_list'),
                                           ('tbss3.outputnode.groupmask',
                                            'inputnode.groupmask'),
                                           ('tbss3.outputnode.meanfa_file',
                                            'inputnode.meanfa_file'),
                                           ('tbss4.outputnode.distance_map',
                                            'inputnode.distance_map')]),
                      (inputnode, tbss_MD, [('md_list',
                                               'inputnode.file_list')]),
                ])
    return tbssproc

Ejemplo n.º 2

tbss_source.inputs.template = '%s/%s_%s.nii'
tbss_source.inputs.template_args = dict(fa_list=[['FA', subject_list, 'FA']],
                                        md_list=[['MD', subject_list, 'MD']])
tbss_source.inputs.sort_filelist = True
"""
TBSS analysis
"""

tbss_all = create_tbss_all()
tbss_all.inputs.inputnode.skeleton_thresh = 0.2

tbssproc = pe.Workflow(name="tbssproc")
tbssproc.base_dir = tbss_dir  # os.path.join(os.path.abspath(resultsDir), ,'tbss', 'l2')
tbssproc.connect(tbss_source, 'fa_list', tbss_all, 'inputnode.fa_list')

tbss_MD = create_tbss_non_FA(name='tbss_MD')
tbss_MD.inputs.inputnode.skeleton_thresh = tbss_all.inputs.inputnode.skeleton_thresh

tbssproc.connect([
    (tbss_all, tbss_MD,
     [('tbss2.outputnode.field_list', 'inputnode.field_list'),
      ('tbss3.outputnode.groupmask', 'inputnode.groupmask'),
      ('tbss3.outputnode.meanfa_file', 'inputnode.meanfa_file'),
      ('tbss4.outputnode.distance_map', 'inputnode.distance_map')]),
    (tbss_source, tbss_MD, [('md_list', 'inputnode.file_list')]),
])
"""
Run the workflow as command line executable
"""

if __name__ == '__main__':

Ejemplo n.º 3

Archivo: tbss_nonFA_NKI.py Proyecto: Conxz/BIT

tbss_source.inputs.sort_filelist = True
tbss_source.inputs.template = '%s.nii.gz'
tbss_source.inputs.template_args = dict(file_list=[[get_nonFAList(subject_list)]],
                                        field_list = [[getfieldList(subject_list)]]
                                        )

"""
Setup data storage area
"""
datasink = pe.Node(interface=nio.DataSink(parameterization=False),name='datasink')
datasink.inputs.base_directory = os.path.abspath(sinkdir)

'''
TBSS analysis
'''
tbss_nonFA = create_tbss_non_FA(name='tbss_'+nonFA)
tbss_nonFA.inputs.inputnode.skeleton_thresh = skeleton_thr
tbss_nonFA.inputs.inputnode.groupmask = os.path.join(sinkdir, 'brain_groupmask.nii.gz')
tbss_nonFA.inputs.inputnode.meanfa_file = os.path.join(sinkdir, 'mean_FA.nii.gz')
tbss_nonFA.inputs.inputnode.distance_map = os.path.join(sinkdir, 'distance_map.nii.gz')

rename_nonfa = pe.Node(util.Rename(format_string='all_'+nonFA+'_skeletonised.nii.gz'), name='renamenonfa')

tbss_nonFA_proc = pe.Workflow(name="tbss_" + nonFA + "_proc")
tbss_nonFA_proc.base_dir = os.path.abspath(tbssDir)
tbss_nonFA_proc.connect([
                (tbss_source, tbss_nonFA,[('file_list','inputnode.file_list'),
                                          ('field_list','inputnode.field_list')
                                          ]),
                (tbss_nonFA, rename_nonfa, [
                                            ('outputnode.projected_nonFA_file', 'in_file'),

Ejemplo n.º 4

Archivo: dmri_tbss_nki.py Proyecto: TheChymera/nipype

tbss_source.inputs.template_args = dict(
    fa_list=[['FA', subjects_list, 'FA']],
    md_list=[['MD', subjects_list, 'MD']])
tbss_source.inputs.sort_filelist = True
"""
TBSS analysis
"""

tbss_all = create_tbss_all()
tbss_all.inputs.inputnode.skeleton_thresh = 0.2

tbssproc = pe.Workflow(name="tbssproc")
tbssproc.base_dir = os.path.join(os.path.abspath(workingdir), 'l2')
tbssproc.connect(tbss_source, 'fa_list', tbss_all, 'inputnode.fa_list')

tbss_MD = create_tbss_non_FA(name='tbss_MD')
tbss_MD.inputs.inputnode.skeleton_thresh = tbss_all.inputs.inputnode.skeleton_thresh

tbssproc.connect([
    (tbss_all, tbss_MD,
     [('tbss2.outputnode.field_list', 'inputnode.field_list'),
      ('tbss3.outputnode.groupmask', 'inputnode.groupmask'),
      ('tbss3.outputnode.meanfa_file',
       'inputnode.meanfa_file'), ('tbss4.outputnode.distance_map',
                                  'inputnode.distance_map')]),
    (tbss_source, tbss_MD, [('md_list', 'inputnode.file_list')]),
])

if __name__ == '__main__':
    tbssproc.write_graph()
    tbssproc.run()