Dicom conversion heuristic script examples

heuristic_ex1.py

def isMoco(dcmfile):
    """Determine if a dicom file is a mocoseries
    """
    import subprocess
    cmd = ['mri_probedicom', '--i', dcmfile, '--t', '8', '103e']
    proc  = subprocess.Popen(cmd,
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE)
    stdout, stderr = proc.communicate()
    return stdout.strip().startswith('MoCoSeries')
    
def infotodict(sdir, dicominfofile):
    """Heuristic evaluator for determining which runs belong where
    """
    import numpy as np
    from glob import glob
    import os
    #raise Exception('Please provide your own heuristic file')
    seq = np.genfromtxt(dicominfofile,dtype=object)
    info = dict(anatomy=dict(highres001=[]), 
                fieldmap=dict(fieldmap128=dict(magnitude=[], phase=[]), 
                              fieldmap64=dict(magnitude=[], phase=[]),
                              fieldmap_resting=dict(magnitude=[], phase=[])),
                diffusion=dict(dwi=[]),
                BOLD=dict(task001_run001=dict(bold=[]), 
                          task002_run001=dict(bold=[]),
                          task003_run001=dict(bold=[]), 
                          task004_run001=dict(bold=[]), 
                          task005_run001=dict(bold=[]),
                          task006_run001=dict(bold=[]),
                          task007_run001=dict(bold=[]),
                          task007_run002=dict(bold=[]),
                          resting=[]))
    first = True
    first_f128 = True
    first_f64 = True
    first_frest = True
    task7 = 0
    for s in seq:
        #MPRAGE
        x,y,sl,nt = (int(s[6]),int(s[7]),int(s[8]),int(s[9]))
        #if (sl == 176) and (nt == 1) and ('MPRAGE' in s[12]):
        if ('MPRAGE' in s[12]):
            info['anatomy']['highres001'].append(int(s[2]))
        elif ('functional' in s[12]) and sl == 27 and nt == 155:
            if not isMoco(glob(os.path.join(sdir,s[1]))[0]):
                info['BOLD']['task002_run001']['bold'].append(int(s[2]))
        elif ('functional' in s[12]) and sl == 27 and nt == 222:
            if not isMoco(glob(os.path.join(sdir,s[1]))[0]):
                info['BOLD']['task003_run001']['bold'].append(int(s[2]))
        elif ('functional' in s[12]) and sl == 27 and nt == 114:
            if not isMoco(glob(os.path.join(sdir,s[1]))[0]):
                info['BOLD']['task004_run001']['bold'].append(int(s[2]))
        elif ('ge_func' in s[12]) and sl == 32 and nt == 324:
            if not isMoco(glob(os.path.join(sdir,s[1]))[0]):
                info['BOLD']['task006_run001']['bold'].append(int(s[2]))
        elif ('ge_func' in s[12]) and sl == 32 and nt == 136:
            if not isMoco(glob(os.path.join(sdir,s[1]))[0]):
                if not task7:
                    info['BOLD']['task007_run001']['bold'].append(int(s[2]))
                    task7 += 1
                else:
                    info['BOLD']['task007_run002']['bold'].append(int(s[2]))
        elif ('functional' in s[12]) and sl == 27 and nt == 156:
            if not isMoco(glob(os.path.join(sdir,s[1]))[0]):
                if first:
                    info['BOLD']['task001_run001']['bold'].append(int(s[2]))
                    first=False
                else:
                    info['BOLD']['task005_run001']['bold'].append(int(s[2]))
        elif s[12].startswith('field_mapping'):
            if 'Resting' in s[12]:
                if first_frest:
                    info['fieldmap']['fieldmap_resting']['magnitude'].append(int(s[2]))
                    first_frest=False
                else:
                    info['fieldmap']['fieldmap_resting']['phase'].append(int(s[2]))
            elif x ==128:
                if first_f128:
                    info['fieldmap']['fieldmap128']['magnitude'].append(int(s[2]))
                    first_f128=False
                else:
                    info['fieldmap']['fieldmap128']['phase'].append(int(s[2]))
            else:
                if first_f64:
                    info['fieldmap']['fieldmap64']['magnitude'].append(int(s[2]))
                    first_f64=False
                else:
                    info['fieldmap']['fieldmap64']['phase'].append(int(s[2]))
        elif 'Resting' in s[12]:
            if not isMoco(glob(os.path.join(sdir,s[1]))[0]):
                info['BOLD']['resting'].append(int(s[2]))
        elif s[12].startswith('DIFFUSION') and sl == 64 and nt ==70:
            info['diffusion']['dwi'].append(int(s[2]))
        else:
            pass
            
    return info
    
if __name__ == '__main__':
    dcmfile = '/mindhive/gablab/rtsmoking/test_retest/brain_data/niftis/sub01s2/dicominfo.txt'
    sdir = '/mindhive/gablab/rtsmoking/test_retest/brain_data/dicoms/sub01s2/'
    info = infotodict(sdir,dcmfile)