Skip to content

fix for SpecifySPMModel #1200

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 3 commits into from
Sep 1, 2015
Merged

fix for SpecifySPMModel #1200

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
3bd70f7
test
MartinPerez Aug 31, 2015
f45e93d
fix
MartinPerez Sep 1, 2015
8d624a4
corrected line of modelgen and added test for variable concatenated e…
MartinPerez Sep 1, 2015
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion nipype/algorithms/modelgen.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -476,7 +476,7 @@ def _concatenate_info(self, infolist):
sum(nscans[0:(i + 1)])
infoout.onsets[j].extend(onsets.tolist())
for j, val in enumerate(info.durations):
if len(val) > 1:
if len(val):
infoout.durations[j].extend(info.durations[j])
if hasattr(info, 'amplitudes') and info.amplitudes:
for j, val in enumerate(info.amplitudes):
Expand Down
20 changes: 19 additions & 1 deletion nipype/algorithms/tests/test_modelgen.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@ def test_modelgen_spm_concat():
filename2 = os.path.join(tempdir, 'test2.nii')
Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename1)
Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename2)
# Test case when only one duration is passed, as being the same for all onsets.
s = SpecifySPMModel()
s.inputs.input_units = 'secs'
s.inputs.concatenate_runs = True
Expand All @@ -78,23 +79,40 @@ def test_modelgen_spm_concat():
yield assert_equal, np.sum(res.outputs.session_info[0]['regress'][0]['val']), 30
yield assert_equal, len(res.outputs.session_info[0]['cond']), 1
yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0])
# Test case of scans as output units instead of seconds
setattr(s.inputs, 'output_units', 'scans')
yield assert_equal, s.inputs.output_units, 'scans'
s.inputs.subject_info = deepcopy(info)
res = s.run()
yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0])/6
# Test case for no concatenation with seconds as output units
s.inputs.concatenate_runs = False
s.inputs.subject_info = deepcopy(info)
s.inputs.output_units = 'secs'
res = s.run()
yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0])
# Test case for variable number of events in separate runs, sometimes unique.
filename3 = os.path.join(tempdir, 'test3.nii')
Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename3)
s.inputs.functional_runs = [filename1, filename2, filename3]
info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]]),
Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2, 4]], durations=[[1, 1], [1, 1]])]
Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2, 4]], durations=[[1, 1], [1, 1]]),
Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]])]
s.inputs.subject_info = deepcopy(info)
res = s.run()
yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1.])
yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1.,])
yield assert_almost_equal, np.array(res.outputs.session_info[1]['cond'][1]['duration']), np.array([1., 1.])
yield assert_almost_equal, np.array(res.outputs.session_info[2]['cond'][1]['duration']), np.array([1.,])
# Test case for variable number of events in concatenated runs, sometimes unique.
s.inputs.concatenate_runs = True
info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]]),
Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2, 4]], durations=[[1, 1], [1, 1]]),
Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]])]
s.inputs.subject_info = deepcopy(info)
res = s.run()
yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1., 1., 1., 1., 1.])
yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1., 1., 1., 1.])
rmtree(tempdir)


Expand Down