Merge branch 'bf/fix_new_structures' into 'master'

Bugfix

See merge request fsl/mist-clean!12

python/autosetup.py

@@ -478,8 +478,8 @@ def generateall(dirs, modalitytypes, scans, csfmask, warp, warpinv, scalarvoxels
     
     common_rn_sn = mist_bin + ' --loglevel=info train ' + \
             setup_common(dirs, modalitytypes, scans_brainstem, csfmask, warp, scalarvoxelsizes, 2.0, 2.0, 1.0)
-    
-    if structures is None or 'red_nucleus' in structures:
+
+    if len(scans_brainstem) > 0 and (structures is None or 'red_nucleus' in structures):
         red_nucleus_priors = setup_red_nucleus(dirs, modalitytypes, scans_brainstem, warpinv, scalarvoxelsizes, medians)
 
         cmds.append(common_rn_sn + ' --mrfweight=10.0 --mrfmeanfrac=0.0 --shape=' + mesh_dir + \
@@ -490,7 +490,7 @@ def generateall(dirs, modalitytypes, scans, csfmask, warp, warpinv, scalarvoxels
                 '/right_red_nucleus.mim --out=' + outdir + '/model_right_red_nucleus.txt ' + \
                 red_nucleus_priors + ' ' + ' '.join(dirs))
 
-    if structures is None or 'substantia_nigra' in structures:
+    if len(scans_brainstem) > 0 and (structures is None or 'substantia_nigra' in structures):
         substantia_nigra_priors = setup_substantia_nigra(dirs, modalitytypes, scans_brainstem, warpinv, scalarvoxelsizes, medians)
 
         cmds.append(common_rn_sn + ' --mrfweight=10.0 --mrfmeanfrac=0.0 --shape=' + mesh_dir + \
@@ -501,7 +501,7 @@ def generateall(dirs, modalitytypes, scans, csfmask, warp, warpinv, scalarvoxels
                 '/right_substantia_nigra.mim --out=' + outdir + '/model_right_substantia_nigra.txt ' + \
                 substantia_nigra_priors + ' ' + ' '.join(dirs))
 
-    if structures is None or 'subthalamic_nucleus' in structures:
+    if len(scans_brainstem) > 0 and (structures is None or 'subthalamic_nucleus' in structures):
         common_stn = mist_bin + ' --loglevel=info train ' + \
                 setup_common(dirs, modalitytypes, scans_brainstem, csfmask, warp, scalarvoxelsizes, 2.0, 2.0, 1.0)