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Merged
merged 2 commits into from
Jun 6, 2014
Merged

Enh/openfmri #850

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e15963e
fix: first untested patch for contrasts
satra Jun 3, 2014
e8b7d58
fix: condition indexing
satra Jun 6, 2014
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14 changes: 10 additions & 4 deletions examples/fmri_openfmri.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -200,13 +200,19 @@ def get_highpass(TR, hpcutoff):
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[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',
Expand Down