Correct bugs linked to parameters change

Author: ocommowi

diffusion/mcm_fiber_atlas_comparison/animaSubjectsMCMFiberPreparation.py

@@ -38,14 +38,13 @@
 parser.add_argument('-s', '--start-subject', type=int, default=1, help="Subject to start with")
 
 parser.add_argument('-i', '--dw-images-prefix', type=str, required=True, help='DW images prefix (folder + basename)')
-parser.add_argument('-d', '--dw-dicom-folders-prefix', type=str, default="", help='Dicom folders prefixes (will append '
-                                                                                  '_n to them')
+parser.add_argument('-d', '--dw-dicom-folders-prefix', type=str, default="", help='Dicom folders prefixes (will append _n to them, where n is the image number)')
 parser.add_argument('-t', '--t1-images-prefix', type=str, required=True, help='T1 images prefix (folder + basename)')
 parser.add_argument('--type', type=str, default="tensor", help="Type of compartment model for fascicles (stick, zeppelin, tensor, noddi, ddi)")
 
 parser.add_argument('--dw-without-reversed-b0', action='store_true', help="No reversed B0 provided with the DWIs")
 
-parser.add_argument('-b', '--bvalue-extract', type=int, default=0, help="Extract only a specific b-value for TractSeg (recommended for CUSP")
+parser.add_argument('-b', '--bvalue-extract', type=int, default=0, help="Extract only a specific b-value for TractSeg (recommended for CUSP)")
 
 args = parser.parse_args()
 

relaxometry/animaT2RelaxometryExtraction.py

@@ -112,7 +112,7 @@
     if os.path.splitext(args.mono_out)[1] == '.gz':
         outPrefix = os.path.splitext(outPrefix)[0]
 
-    monoT2Command = [animaDir + "animaT2EPGRelaxometryEstimation", "-l", inputImage, "-o", args.mono_out, "--tr", str(args.tr_value),
+    monoT2Command = [animaDir + "animaT2EPGRelaxometryEstimation", "-i", inputImage, "-o", args.mono_out, "--tr", str(args.tr_value),
                      "-e", str(args.echo_spacing), "--out-b1", outPrefix + "_B1.nrrd", "-O", outPrefix + "_M0.nrrd"]
 
     if maskImage != "":