Option to specify internal reference in fsl_mrs.

fsl_mrs/scripts/fsl_mrs

@@ -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,