fix: condition indexing

Author: satra

examples/fmri_openfmri.py

@@ -121,15 +121,15 @@ def analyze_openfmri_dataset(data_dir, subject=None, model_id=None,
     Set up openfmri data specific components
     """
 
-    subjects = [path.split(os.path.sep)[-1] for path in
-                glob(os.path.join(data_dir, 'sub*'))]
+    subjects = sorted([path.split(os.path.sep)[-1] for path in
+                       glob(os.path.join(data_dir, 'sub*'))])
 
     infosource = pe.Node(niu.IdentityInterface(fields=['subject_id',
                                                        'model_id',
                                                        'task_id']),
                          name='infosource')
     if subject is None:
-        infosource.iterables = [('subject_id', subjects[:2]),
+        infosource.iterables = [('subject_id', subjects),
                                 ('model_id', [model_id]),
                                 ('task_id', [task_id])]
     else:
@@ -201,14 +201,18 @@ def get_contrasts(contrast_file, task_id, conds):
         import numpy as np
         contrast_def = np.genfromtxt(contrast_file, dtype=object)
         if len(contrast_def.shape) == 1:
-            contrast_def = [contrast_def]
+            contrast_def = contrast_def[None, :]
         contrasts = []
         for row in contrast_def:
             if row[0] != 'task%03d' % task_id:
                 continue
-            con = [row[1], 'T', ['cond%03d' % i  for i in range(len(conds))],
+            con = [row[1], 'T', ['cond%03d' % (i + 1)  for i in range(len(conds))],
                    row[2:].astype(float).tolist()]
             contrasts.append(con)
+        # add auto contrasts for each column
+        for i, cond in enumerate(conds):
+            con = [cond, 'T', ['cond%03d' % (i + 1)], [1]]
+            contrasts.append(con)
         return contrasts
 
     contrastgen = pe.Node(niu.Function(input_names=['contrast_file',
@@ -260,8 +264,6 @@ def get_contrasts(contrast_file, task_id, conds):
     """
 
     def sort_copes(files):
-        from nipype.utils.filemanip import filename_to_list
-        files = filename_to_list(files)
         numelements = len(files[0])
         outfiles = []
         for i in range(numelements):
@@ -271,8 +273,6 @@ def sort_copes(files):
         return outfiles
 
     def num_copes(files):
-        from nipype.utils.filemanip import filename_to_list
-        files = filename_to_list(files)
         return len(files)
 
     pickfirst = lambda x: x[0]