def test_L2Model_outputs():
output_map = dict(design_grp=dict(),
design_con=dict(),
design_mat=dict(),
)
outputs = L2Model.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_L2Model_outputs():
output_map = dict(
design_con=dict(),
design_grp=dict(),
design_mat=dict(),
)
outputs = L2Model.output_spec()
for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_L2Model_inputs():
input_map = dict(ignore_exception=dict(nohash=True,
usedefault=True,
),
num_copes=dict(mandatory=True,
),
)
inputs = L2Model.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def test_L2Model_inputs():
input_map = dict(
ignore_exception=dict(
nohash=True,
usedefault=True,
),
num_copes=dict(mandatory=True, ),
)
inputs = L2Model.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def secondlevel_wf(subject_id, sink_directory, name='GLM1_scndlvl_wf'):
scndlvl_wf = Workflow(name='scndlvl_wf')
base_dir = os.path.abspath('/home/data/madlab/data/mri/wmaze/')
contrasts = [
'all_before_B_corr', 'all_before_B_incorr', 'all_remaining',
'all_corr_minus_all_incorr', 'all_incorr_minus_all_corr'
]
cnt_file_list = []
for curr_contrast in contrasts:
cnt_file_list.append(
glob(
os.path.join(
base_dir,
'frstlvl/model_GLM1/{0}/modelfit/contrasts/_estimate_model*/cope??_{1}.nii.gz'
.format(subject_id, curr_contrast))))
dof_runs = [[], [], [], [], []]
for i, curr_file_list in enumerate(cnt_file_list):
if not isinstance(curr_file_list, list):
curr_file_list = [curr_file_list]
for curr_file in curr_file_list:
dof_runs[i].append(
curr_file.split('/')[-2][-1]) #grabs the estimate_model #
info = dict(copes=[['subject_id', contrasts]],
varcopes=[['subject_id', contrasts]],
mask_file=[['subject_id', 'aparc+aseg_thresh']],
dof_files=[['subject_id', dof_runs, 'dof']])
#datasource node to get task_mri and motion-noise files
datasource = Node(DataGrabber(infields=['subject_id'],
outfields=info.keys()),
name='datasource')
datasource.inputs.template = '*'
datasource.inputs.subject_id = subject_id
datasource.inputs.base_directory = os.path.abspath(
'/home/data/madlab/data/mri/wmaze/')
datasource.inputs.field_template = dict(
copes=
'frstlvl/model_GLM1/%s/modelfit/contrasts/_estimate_model*/cope*_%s.nii.gz',
varcopes=
'frstlvl/model_GLM1/%s/modelfit/contrasts/_estimate_model*/varcope*_%s.nii.gz',
mask_file='preproc/%s/ref/_fs_threshold20/%s*_thresh.nii',
dof_files='frstlvl/model_GLM1/%s/modelfit/dofs/_estimate_model%s/%s')
datasource.inputs.template_args = info
datasource.inputs.sort_filelist = True
datasource.inputs.ignore_exception = False
datasource.inputs.raise_on_empty = True
#inputspec to deal with copes and varcopes doublelist issues
fixedfx_inputspec = Node(IdentityInterface(
fields=['copes', 'varcopes', 'dof_files'], mandatory_inputs=True),
name='fixedfx_inputspec')
scndlvl_wf.connect(datasource, ('copes', doublelist), fixedfx_inputspec,
'copes')
scndlvl_wf.connect(datasource, ('varcopes', doublelist), fixedfx_inputspec,
'varcopes')
scndlvl_wf.connect(datasource, ('dof_files', doublelist),
fixedfx_inputspec, 'dof_files')
#merge all of copes into a single matrix across subject runs
copemerge = MapNode(Merge(), iterfield=['in_files'], name='copemerge')
copemerge.inputs.dimension = 't'
copemerge.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
copemerge.inputs.ignore_exception = False
copemerge.inputs.output_type = 'NIFTI_GZ'
copemerge.inputs.terminal_output = 'stream'
scndlvl_wf.connect(fixedfx_inputspec, 'copes', copemerge, 'in_files')
#generate DOF volume for second level
gendofvolume = Node(Function(input_names=['dof_files', 'cope_files'],
output_names=['dof_volumes'],
function=get_dofvolumes),
name='gendofvolume')
gendofvolume.inputs.ignore_exception = False
scndlvl_wf.connect(fixedfx_inputspec, 'dof_files', gendofvolume,
'dof_files')
scndlvl_wf.connect(copemerge, 'merged_file', gendofvolume, 'cope_files')
#merge all of the varcopes into a single matrix across subject runs per voxel
varcopemerge = MapNode(Merge(),
iterfield=['in_files'],
name='varcopemerge')
varcopemerge.inputs.dimension = 't'
varcopemerge.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
varcopemerge.inputs.ignore_exception = False
varcopemerge.inputs.output_type = 'NIFTI_GZ'
varcopemerge.inputs.terminal_output = 'stream'
scndlvl_wf.connect(fixedfx_inputspec, 'varcopes', varcopemerge, 'in_files')
#define contrasts from the names of the copes
getcontrasts = Node(Function(input_names=['data_inputs'],
output_names=['contrasts'],
function=get_contrasts),
name='getcontrasts')
getcontrasts.inputs.ignore_exception = False
scndlvl_wf.connect(datasource, ('copes', doublelist), getcontrasts,
'data_inputs')
#rename output files to be more descriptive
getsubs = Node(Function(input_names=['subject_id', 'cons'],
output_names=['subs'],
function=get_subs),
name='getsubs')
getsubs.inputs.ignore_exception = False
getsubs.inputs.subject_id = subject_id
scndlvl_wf.connect(getcontrasts, 'contrasts', getsubs, 'cons')
#l2model node for fixed effects analysis (aka within subj across runs)
l2model = MapNode(L2Model(), iterfield=['num_copes'], name='l2model')
l2model.inputs.ignore_exception = False
scndlvl_wf.connect(datasource, ('copes', num_copes), l2model, 'num_copes')
#FLAMEO Node to run the fixed effects analysis
flameo_fe = MapNode(FLAMEO(),
iterfield=[
'cope_file', 'var_cope_file', 'dof_var_cope_file',
'design_file', 't_con_file', 'cov_split_file'
],
name='flameo_fe')
flameo_fe.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
flameo_fe.inputs.ignore_exception = False
flameo_fe.inputs.log_dir = 'stats'
flameo_fe.inputs.output_type = 'NIFTI_GZ'
flameo_fe.inputs.run_mode = 'fe'
flameo_fe.inputs.terminal_output = 'stream'
scndlvl_wf.connect(varcopemerge, 'merged_file', flameo_fe, 'var_cope_file')
scndlvl_wf.connect(l2model, 'design_mat', flameo_fe, 'design_file')
scndlvl_wf.connect(l2model, 'design_con', flameo_fe, 't_con_file')
scndlvl_wf.connect(l2model, 'design_grp', flameo_fe, 'cov_split_file')
scndlvl_wf.connect(gendofvolume, 'dof_volumes', flameo_fe,
'dof_var_cope_file')
scndlvl_wf.connect(datasource, 'mask_file', flameo_fe, 'mask_file')
scndlvl_wf.connect(copemerge, 'merged_file', flameo_fe, 'cope_file')
#outputspec node
scndlvl_outputspec = Node(IdentityInterface(
fields=['res4d', 'copes', 'varcopes', 'zstats', 'tstats'],
mandatory_inputs=True),
name='scndlvl_outputspec')
scndlvl_wf.connect(flameo_fe, 'res4d', scndlvl_outputspec, 'res4d')
scndlvl_wf.connect(flameo_fe, 'copes', scndlvl_outputspec, 'copes')
scndlvl_wf.connect(flameo_fe, 'var_copes', scndlvl_outputspec, 'varcopes')
scndlvl_wf.connect(flameo_fe, 'zstats', scndlvl_outputspec, 'zstats')
scndlvl_wf.connect(flameo_fe, 'tstats', scndlvl_outputspec, 'tstats')
#datasink node
sinkd = Node(DataSink(), name='sinkd')
sinkd.inputs.base_directory = sink_directory
sinkd.inputs.container = subject_id
scndlvl_wf.connect(scndlvl_outputspec, 'copes', sinkd, 'fixedfx.@copes')
scndlvl_wf.connect(scndlvl_outputspec, 'varcopes', sinkd,
'fixedfx.@varcopes')
scndlvl_wf.connect(scndlvl_outputspec, 'tstats', sinkd, 'fixedfx.@tstats')
scndlvl_wf.connect(scndlvl_outputspec, 'zstats', sinkd, 'fixedfx.@zstats')
scndlvl_wf.connect(scndlvl_outputspec, 'res4d', sinkd, 'fixedfx.@pvals')
scndlvl_wf.connect(getsubs, 'subs', sinkd, 'substitutions')
return scndlvl_wf
inputspec.inputs.brain_mask = '/home/data/madlab/data/mri/wmaze/wmaze_T1_template/wmaze_grptemplate_mask.nii.gz' #anatomical group template mask
inputspec.inputs.run_mode = 'flame1'
group_wf.connect(datasource, 'copes', inputspec, 'copes')
group_wf.connect(datasource, 'varcopes', inputspec, 'varcopes')
#node to concatenate varcopes into single image across time
grp_merge_varcopes = Node(fsl.utils.Merge(), name='grp_merge_varcopes')
grp_merge_varcopes.inputs.dimension = 't' #concatenate across time
grp_merge_varcopes.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
grp_merge_varcopes.inputs.ignore_exception = False
grp_merge_varcopes.inputs.output_type = 'NIFTI_GZ'
grp_merge_varcopes.inputs.terminal_output = 'stream'
group_wf.connect(inputspec, 'varcopes', grp_merge_varcopes, 'in_files')
#node for group-specific level 2 model
grp_l2model = Node(L2Model(), name='grp_l2model')
grp_l2model.inputs.ignore_exception = False
group_wf.connect(inputspec, ('copes', get_len), grp_l2model, 'num_copes')
#node to concatenate copes into single image across time
grp_merge_copes = Node(fsl.utils.Merge(), name='grp_merge_copes')
grp_merge_copes.inputs.dimension = 't' #concatenate across time
grp_merge_copes.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
grp_merge_copes.inputs.ignore_exception = False
grp_merge_copes.inputs.output_type = 'NIFTI_GZ'
grp_merge_copes.inputs.terminal_output = 'stream'
group_wf.connect(inputspec, 'copes', grp_merge_copes, 'in_files')
#node for Randomise
grp_randomise = Node(fsl.Randomise(), name='grp_randomise')
grp_randomise.inputs.environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}