moved euler to group2

run.py

@@ -40,9 +40,9 @@ def run(command, env={}, ignore_errors=False):
                     'Multiple participant level analyses can be run independently '
                     '(in parallel) using the same output_dir. '
                     '"group1" creates study specific group template. '
-                    '"group2" exports group stats tables for cortical parcellation and subcortical segmentation.'
-                    '"group3" exports euler numbers.',
-                    choices=['participant', 'group1', 'group2', 'group3'])
+                    '"group2" exports group stats tables for cortical parcellation, subcortical segmentation '
+                                           'a table with euler numbers.',
+                    choices=['participant', 'group1', 'group2'])
 parser.add_argument('--participant_label', help='The label of the participant that should be analyzed. The label '
                     'corresponds to sub-<participant_label> from the BIDS spec '
                     '(so it does not include "sub-"). If this parameter is not '
@@ -492,13 +492,11 @@ def run(command, env={}, ignore_errors=False):
         print("\nTable export finished for %d subjects/sessions." % len(subjects))
 
     else:
-        print("\nNo subjects included in the analysis. Skipping group2 level.")
+        print("\nNo subjects included in the analysis. Skipping group2 level stats tables.")
 
 
-elif args.analysis_level == "group3":  # extract euler number
     # This extracts the euler numbers for the orig.nofix surfaces from the recon-all.log file
     # see Rosen et al. (2017), https://www.biorxiv.org/content/early/2017/10/01/125161
-
     def extract_euler(logfile):
         with open(logfile) as fi:
             logtext = fi.read()
@@ -509,10 +507,9 @@ def extract_euler(logfile):
         lh_euler, rh_euler = results[0]
         return int(lh_euler), int(rh_euler)
 
-    euler_out_path = os.path.join(output_dir, "00_group3_quality")
-    if not os.path.isdir(euler_out_path):
-        os.makedirs(euler_out_path)
-    euler_out_file = os.path.join(euler_out_path, "euler.tsv")
+
+
+    euler_out_file = os.path.join(table_dir, "euler.tsv")
     print("Writing euler tables to %s." % euler_out_file)
 
     # get freesurfer subjects
@@ -534,6 +531,7 @@ def extract_euler(logfile):
                                         columns=["subject", "lh_euler", "rh_euler"])
             df = df.append(df_subject)
         df["mean_euler_bh"] = df[["lh_euler", "rh_euler"]].mean(1)
+        df.sort_values("subject", inplace=True)
         df.to_csv(euler_out_file, sep="\t", index=False)
     else:
-        print("\nNo subjects included in the analysis. Skipping group3 level.")
+        print("\nNo subjects included in the analysis. Skipping group2 level euler number table.")