diff --git a/pyris/bin/pyris b/pyris/bin/pyris
index 2746e92..e10e918 100644
--- a/pyris/bin/pyris
+++ b/pyris/bin/pyris
@@ -160,7 +160,7 @@ if args.config is not None:
     axisdir     = os.path.join( cf.get( 'Data', 'output' ), 'axis'      )
     migdir      = os.path.join( cf.get( 'Data', 'output' ), 'migration' )
     bardir      = os.path.join( cf.get( 'Data', 'output' ), 'bars'      )
-    if not args.raw_mask_import:
+    if args.segmentation or args.bars:
         landsat_dirs = sorted( [ os.path.join(cf.get('Data','input'), f) for f in os.listdir(cf.get('Data','input'))
                              if os.path.isdir( os.path.join(cf.get('Data','input'), f) ) ] )
     # log file
@@ -294,22 +294,28 @@ if args.migration:
         print(); print(title); print('-'*len(title))
         axisfiles = [ os.path.join( axisdir, f ) for f in sorted( os.listdir( axisdir ) ) ]
         migration_rates( axisfiles, migdir, columns=(0,1), show=args.show, pfreq=pf )
-    elif args.axis_files is not None and args.config is None:
+    elif args.axis_dir is not None and args.axis_files is not None:
+        raise ParserException('--axis-files or --axis-dir cannot be provided together')
+    elif args.axis_files is not None:
         if not os.path.isdir( args.output_dir ): os.makedirs( args.output_dir )
         title = 'Computing migration rates from files: %s' % args.axis_files
-        print(); print(title); print('-'*len(title))
-        migration_rates( args.axis_files, args.output_dir, columns=args.axis_columns, show=args.show, pfreq=pf )
-    elif args.axis_dir is not None and args.config is None:
+        print(); print(title); print('-'*len(title)) 
+        axis_files = []
+        for f in args.axis_files:
+            path, file = os.path.split( f )
+            if path == '' and args.config is not None:
+                axis_files.append( os.path.join( axisdir, f ) )
+            else:
+                axis_files.append( f )
+        migration_rates( axis_files, args.output_dir, columns=args.axis_columns, show=args.show, pfreq=pf )
+    elif args.axis_dir is not None:
         axis_files = [ os.path.join(args.axis_dir, f) for f in sorted(os.listdir(args.axis_dir)) ]
         if not os.path.isdir( args.output_dir ): os.makedirs( args.output_dir )
         title = 'Computing migration rates from directory: %s' % args.axis_dir
         print(); print(title); print('-'*len(title))
         migration_rates( axis_files, args.output_dir, columns=args.axis_columns, show=args.show, pfreq=pf )
     else:
-        if args.axis_dir is not None and args.axis_files is not None:
-            raise ParserException('--axis-files or --axis-dir cannot be provided together')
-        else:
-            raise ParserException('Either --axis-files, --axis-dir or config must be provided')
+        raise ParserException('Either --axis-files, --axis-dir or config must be provided')
 
 # Bars Position
 # -------------
@@ -317,6 +323,7 @@ if args.bars:
     if not os.path.isdir( bardir ): os.makedirs( bardir )
     from pyris import bars_detection
     title = 'Decesting bars from centerlines in internal directory: %s' % cf.get( 'Data', 'output' )
+    print(); print(title); print('-'*len(title))
     bars_detection( landsat_dirs, geodir, axisdir, migdir, bardir, show=args.show )
 
 # print elapsed time