change mindboggle123 recon all 3T flag to include more generic string argument

changed previous pull request (include recon all's 3T flag within mindboggle123) to add a more generic string argument which adds multiple recon all flags

Author: PeerHerholz

mindboggle/mindboggle123

@@ -87,9 +87,9 @@ adv_args.add_argument("--fs_openmp", dest="openmp",
 adv_args.add_argument("--fs_T2image", dest="T2image",
                       type=str,
                       help="Optional T2 image to use with FreeSurfer")
-adv_args.add_argument("--fs_3T", dest="T3",
-					  type=str,
-					  help="Enable recon-all's 3T option (nu intensity correction params & special schwartz atlas) ")
+adv_args.add_argument("--fs_flags", dest="fs_flags",
+					  type=str, nargs='+',
+					  help="include additional recon-all flags like e.g. '-nuintensitycor-3T' ")
 adv_args.add_argument("--ants_num_threads", dest="num_threads",
                       default=1, type=int,
                       help="Number of threads to use with ANTs")
@@ -147,8 +147,8 @@ if args.openmp and args.openmp > 1:
 if args.T2image:
     reconall.inputs.T2_file = args.T2image
     reconall.inputs.use_T2 = True
-if args.T3:
-	reconall.inputs.flags = '-nuintensitycor-3T'
+if args.fs_flags:
+	reconall.inputs.flags = fs_flags
 
 # ----------------------------------------------------------------------------
 # Use antsCorticalThickness.sh to generate segmentations of structural data: