New options in fsl_mrs.

fsl_mrs/core/MRS.py

@@ -252,13 +252,13 @@ class MRS(object):
 
         
     # Helper functions
-    def processForFitting(self,ppmlim=(.2,4.2),):
+    def processForFitting(self,ppmlim=(.2,4.2),ind_scaling=None):
         """ Apply rescaling and run the conjugation checks"""
         self.check_FID(ppmlim=ppmlim,repair=True)
         self.check_Basis(ppmlim=ppmlim,repair=True)
-        self.rescaleForFitting()
+        self.rescaleForFitting(ind_scaling=ind_scaling)
 
-    def rescaleForFitting(self,scale=100):
+    def rescaleForFitting(self,scale=100,ind_scaling=None):
         """ Apply rescaling across data, basis and H20"""
         
         scaledFID,scaling = misc.rescale_FID(self.FID,scale=scale)
@@ -267,7 +267,17 @@ class MRS(object):
             self.H2O *= scaling
 
         if self.basis is not None:
-            self.basis,scaling_basis = misc.rescale_FID(self.basis,scale=scale)
+            if ind_scaling is None:
+                self.basis,scaling_basis = misc.rescale_FID(self.basis,scale=scale)
+            else:
+                index = [self.names.index(n) for n in ind_scaling]
+                mask = np.zeros_like(self.names,dtype=bool)
+                mask[index] = True
+                self.basis[:,~mask],scaling_basis = misc.rescale_FID(self.basis[:,~mask],scale=scale)
+                scaling_basis = [scaling_basis]
+                for idx in index:
+                    self.basis[:,idx],tmp = misc.rescale_FID(self.basis[:,idx],scale=scale)
+                    scaling_basis.append(tmp)
         else:
             scaling_basis = None
 

fsl_mrs/scripts/fsl_mrs

@@ -77,6 +77,12 @@ def main():
     fitting_args.add_argument('--lorentzian', action="store_true",
                               help='Enable purely lorentzian broadening'
                                    ' (default is Voigt)')
+    fitting_args.add_argument('--ind_scale', default=None, type=str,
+                              nargs='+',
+                              help='List of basis spectra to scale'
+                                   ' independently of other basis spectra.')
+    fitting_args.add_argument('--disable_MH_priors', action="store_true",
+                              help="Disable MH priors.")
 
     # ADDITIONAL OPTIONAL ARGUMENTS
     optional.add_argument('--t1', type=str, default=None, metavar='IMAGE',
@@ -244,7 +250,7 @@ def main():
 
     # Rescale FID, H2O and basis to have nice range
     if not args.no_rescale:
-        mrs.rescaleForFitting()
+        mrs.rescaleForFitting(ind_scaling=args.ind_scale)
 
     # Do phase correction
     if args.phase_correct:
@@ -278,18 +284,21 @@ def main():
         G = [i+max(metab_groups)+1 for i in range(nMM)]
         metab_groups += G
 
+    # Choose fitting lineshape model.
     if args.lorentzian:
         Fitargs = {'ppmlim': ppmlim,
                    'method': args.algo,
                    'baseline_order': args.baseline_order,
                    'metab_groups': metab_groups,
-                   'model': 'lorentzian'}
+                   'model': 'lorentzian',
+                   'disable_mh_priors': args.disable_MH_priors}
     else:
         Fitargs = {'ppmlim': ppmlim,
                    'method': args.algo,
                    'baseline_order': args.baseline_order,
                    'metab_groups': metab_groups,
-                   'model': 'voigt'}
+                   'model': 'voigt',
+                   'disable_mh_priors': args.disable_MH_priors}
 
     if args.verbose:
         print(mrs)