Commit 589c1f16 authored by William Clarke's avatar William Clarke
Browse files

Option to specify internal reference in fsl_mrs.

parent becfa99d
......@@ -76,6 +76,8 @@ def main():
help='Echo time for relaxation correction (ms)')
optional.add_argument('--tissue_fractions',type=float,nargs=3,default=[0.5,0.5,0.0],metavar='GM WM CSF',
help='Fractional tissue volumes for WM, GM, CSF. Defaults to 0.5, 0.5, 0.0.')
optional.add_argument('--internal_ref',type=str,default=['Cr','PCr'],nargs='+',
help='Metabolite(s) used as an internal reference. Defaults to tCr (Cr+PCr).')
optional.add_argument('--central_frequency',default=None,type=float,
help='central frequency in Hz')
optional.add_argument('--dwell_time',default=None,type=float,
......@@ -295,11 +297,11 @@ def main():
echotime = None
# Internal and Water quantification if requested
if (mrs.H2O is None) or (echotime is None):
res.calculateConcScaling(mrs,referenceMetab=['Cr','PCr'])
res.calculateConcScaling(mrs,referenceMetab=args.internal_ref)
else:
tfrac = {'WM':args.tissue_fractions[0],'GM':args.tissue_fractions[1],'CSF':args.tissue_fractions[2]}
res.calculateConcScaling(mrs,
referenceMetab=['Cr','PCr'],
referenceMetab=args.internal_ref,
waterRefFID=mrs.H2O,
tissueFractions=tfrac,
TE=echotime,
......
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