def test_MRISPreproc_outputs():
output_map = dict(out_file=dict(), )
outputs = MRISPreproc.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_MRISPreproc_outputs():
output_map = dict(out_file=dict(),
)
outputs = MRISPreproc.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_MRISPreproc_inputs():
input_map = dict(surf_dir=dict(argstr='--surfdir %s',
),
vol_measure_file=dict(argstr='--iv %s %s...',
),
fsgd_file=dict(xor=('subjects', 'fsgd_file', 'subject_file'),
argstr='--fsgd %s',
),
fwhm=dict(xor=['num_iters'],
argstr='--fwhm %f',
),
fwhm_source=dict(xor=['num_iters_source'],
argstr='--fwhm-src %f',
),
surf_measure=dict(xor=('surf_measure', 'surf_measure_file', 'surf_area'),
argstr='--meas %s',
),
subject_file=dict(xor=('subjects', 'fsgd_file', 'subject_file'),
argstr='--f %s',
),
surf_measure_file=dict(xor=('surf_measure', 'surf_measure_file', 'surf_area'),
argstr='--is %s...',
),
source_format=dict(argstr='--srcfmt %s',
),
subjects=dict(xor=('subjects', 'fsgd_file', 'subject_file'),
argstr='--s %s...',
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
hemi=dict(mandatory=True,
argstr='--hemi %s',
),
surf_area=dict(xor=('surf_measure', 'surf_measure_file', 'surf_area'),
argstr='--area %s',
),
args=dict(argstr='%s',
),
terminal_output=dict(mandatory=True,
nohash=True,
),
num_iters_source=dict(xor=['fwhm_source'],
argstr='--niterssrc %d',
),
smooth_cortex_only=dict(argstr='--smooth-cortex-only',
),
subjects_dir=dict(),
num_iters=dict(xor=['fwhm'],
argstr='--niters %d',
),
proj_frac=dict(argstr='--projfrac %s',
),
target=dict(mandatory=True,
argstr='--target %s',
),
out_file=dict(argstr='--out %s',
genfile=True,
),
environ=dict(nohash=True,
usedefault=True,
),
)
inputs = MRISPreproc.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_MRISPreproc_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
fsgd_file=dict(argstr='--fsgd %s',
xor=('subjects', 'fsgd_file', 'subject_file'),
),
fwhm=dict(argstr='--fwhm %f',
xor=['num_iters'],
),
fwhm_source=dict(argstr='--fwhm-src %f',
xor=['num_iters_source'],
),
hemi=dict(argstr='--hemi %s',
mandatory=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
num_iters=dict(argstr='--niters %d',
xor=['fwhm'],
),
num_iters_source=dict(argstr='--niterssrc %d',
xor=['fwhm_source'],
),
out_file=dict(argstr='--out %s',
genfile=True,
),
proj_frac=dict(argstr='--projfrac %s',
),
smooth_cortex_only=dict(argstr='--smooth-cortex-only',
),
source_format=dict(argstr='--srcfmt %s',
),
subject_file=dict(argstr='--f %s',
xor=('subjects', 'fsgd_file', 'subject_file'),
),
subjects=dict(argstr='--s %s...',
xor=('subjects', 'fsgd_file', 'subject_file'),
),
subjects_dir=dict(),
surf_area=dict(argstr='--area %s',
xor=('surf_measure', 'surf_measure_file', 'surf_area'),
),
surf_dir=dict(argstr='--surfdir %s',
),
surf_measure=dict(argstr='--meas %s',
xor=('surf_measure', 'surf_measure_file', 'surf_area'),
),
surf_measure_file=dict(argstr='--is %s...',
xor=('surf_measure', 'surf_measure_file', 'surf_area'),
),
target=dict(argstr='--target %s',
mandatory=True,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
vol_measure_file=dict(argstr='--iv %s %s...',
),
)
inputs = MRISPreproc.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 genFreesurferSBMglmWF(name='fsSBM',
base_dir=op.abspath('.'),
group_sublist=[],
model_dir=None,
model_info={'Model1': 'dods'},
design_input='fsgd',
fs_subjects_dir='/data/analyses/work_in_progress/freesurfer/fsmrishare-flair6.0/',
fwhm=[0.0, 10.0],
measure_list=['thickness', 'area'],
target_atlas='fsaverage',
target_atlas_surfreg='sphere.reg',
correction_method='FDR'):
wf = Workflow(name)
wf.base_dir = base_dir
# Node: model List
modelList = Node(IdentityInterface(fields=['model_name'], mandatory_inputs=True),
name='modelList')
modelList.iterables = ('model_name', list(model_info.keys()))
# Grab fsgd or design mat and contrast mtx files from model_dir
fileList_temp_args = {'contrast_files': [['model_name', '*.mtx']],
'contrast_sign_files': [['model_name', '*.mdtx']]}
if design_input == 'fsgd':
fileList_temp_args['fsgd_file'] = [['model_name', '*.fsgd']]
elif design_input == 'design_mat':
fileList_temp_args['design_mat'] = [['model_name', 'X.mat']]
fileList = Node(DataGrabber(infields=['model_name'],
outfields=list(fileList_temp_args.keys())),
name="fileList")
fileList.inputs.base_directory = model_dir
fileList.inputs.ignore_exception = False
fileList.inputs.raise_on_empty = True
fileList.inputs.sort_filelist = True
fileList.inputs.template = '%s/%s'
fileList.inputs.template_args = fileList_temp_args
wf.connect(modelList, "model_name", fileList, "model_name")
# preproc for each hemisphere to produce concatenated file for glmfit and
# also a mean map
# Define a few other iterables
measList = Node(IdentityInterface(fields=['measure'],
mandatory_inputs=True),
name='measList')
measList.iterables = ('measure', measure_list)
smoothList = Node(IdentityInterface(fields=['fwhm'],
mandatory_inputs=True),
name='smoothList')
smoothList.iterables = ('fwhm', fwhm)
surfaces = ['inflated', 'pial']
plotSurfList = Node(IdentityInterface(fields=['surf']),
name='plotSurfList')
plotSurfList.iterables = ('surf', surfaces)
# MRI_preproc
lhSBMpreproc = MapNode(MRISPreproc(),
name='lhSBMpreproc',
iterfield=['args', 'out_file'])
lhSBMpreproc.inputs.subjects_dir = fs_subjects_dir
lhSBMpreproc.inputs.target = target_atlas
lhSBMpreproc.inputs.hemi = 'lh'
lhSBMpreproc.inputs.args = ['', '--mean']
lhSBMpreproc.inputs.out_file = ['{}.lh.{}.mgh'.format(out_name, target_atlas) for out_name in ['stacked', 'mean']]
lhSBMpreproc.inputs.subjects = group_sublist
wf.connect(measList, "measure", lhSBMpreproc, "surf_measure")
rhSBMpreproc = MapNode(MRISPreproc(),
name='rhSBMpreproc',
iterfield=['args', 'out_file'])
rhSBMpreproc.inputs.subjects_dir = fs_subjects_dir
rhSBMpreproc.inputs.target = target_atlas
rhSBMpreproc.inputs.hemi = 'rh'
rhSBMpreproc.inputs.args = ['', '--mean']
rhSBMpreproc.inputs.out_file = ['{}.rh.{}.mgh'.format(out_name, target_atlas) for out_name in ['stacked', 'mean']]
rhSBMpreproc.inputs.subjects = group_sublist
wf.connect(measList, "measure", rhSBMpreproc, "surf_measure")
# Create smoothed mean maps for each non-zero fwhm
non_zero_fwhm = [val for val in fwhm if val != 0.0]
lhSmoothMean = MapNode(SurfaceSmooth(),
name='lhSmoothMean',
iterfield=['fwhm', 'out_file'])
lhSmoothMean.inputs.subject_id = target_atlas
lhSmoothMean.inputs.hemi = 'lh'
lhSmoothMean.inputs.subjects_dir = fs_subjects_dir
lhSmoothMean.inputs.fwhm = non_zero_fwhm
lhSmoothMean.inputs.cortex = True
lhSmoothMean.inputs.out_file = ['mean.lh.fwhm{}.{}.mgh'.format(str(int(val)), target_atlas) for val in non_zero_fwhm]
wf.connect(lhSBMpreproc, ('out_file', getElementFromList, 1), lhSmoothMean, 'in_file')
rhSmoothMean = MapNode(SurfaceSmooth(),
name='rhSmoothMean',
iterfield=['fwhm', 'out_file'])
rhSmoothMean.inputs.subject_id = target_atlas
rhSmoothMean.inputs.hemi = 'rh'
rhSmoothMean.inputs.subjects_dir = fs_subjects_dir
rhSmoothMean.inputs.fwhm = non_zero_fwhm
rhSmoothMean.inputs.cortex = True
rhSmoothMean.inputs.out_file = ['mean.rh.fwhm{}.{}.mgh'.format(str(int(val)), target_atlas) for val in non_zero_fwhm]
wf.connect(rhSBMpreproc, ('out_file', getElementFromList, 1), rhSmoothMean, 'in_file')
# For each concatenated surfaces produced by the SBMpreproc, run glmfit
if correction_method == 'FDR':
save_res = False
elif correction_method == 'perm':
save_res = True
if design_input == 'fsgd':
fsgdInput = Node(Function(input_names=['item1', 'item2'],
output_names=['out_tuple'],
function=createTuple2),
name='fsgdInput')
wf.connect(fileList, 'fsgd_file', fsgdInput, 'item1')
wf.connect(modelList, ('model_name', getValFromDict, model_info),
fsgdInput, 'item2')
lhSBMglmfit = Node(GLMFit(),
name='lhSBMglmfit')
lhSBMglmfit.inputs.subjects_dir = fs_subjects_dir
lhSBMglmfit.inputs.surf = True
lhSBMglmfit.inputs.subject_id = target_atlas
lhSBMglmfit.inputs.hemi = 'lh'
lhSBMglmfit.inputs.cortex = True
lhSBMglmfit.inputs.save_residual = save_res
wf.connect(smoothList, 'fwhm', lhSBMglmfit, 'fwhm')
wf.connect(lhSBMpreproc, ('out_file', getElementFromList, 0), lhSBMglmfit, 'in_file')
if design_input == 'fsgd':
wf.connect(fsgdInput, 'out_tuple', lhSBMglmfit, 'fsgd')
elif design_input == 'design_mat':
wf.connect(fileList, 'design_mat', lhSBMglmfit, 'design')
wf.connect(fileList, 'contrast_files', lhSBMglmfit, 'contrast')
rhSBMglmfit = Node(GLMFit(),
name='rhSBMglmfit')
rhSBMglmfit.inputs.subjects_dir = fs_subjects_dir
rhSBMglmfit.inputs.surf = True
rhSBMglmfit.inputs.subject_id = target_atlas
rhSBMglmfit.inputs.hemi = 'rh'
rhSBMglmfit.inputs.cortex = True
rhSBMglmfit.inputs.save_residual = save_res
wf.connect(smoothList, 'fwhm', rhSBMglmfit, 'fwhm')
wf.connect(rhSBMpreproc, ('out_file', getElementFromList, 0), rhSBMglmfit, 'in_file')
if design_input == 'fsgd':
wf.connect(fsgdInput, 'out_tuple', rhSBMglmfit, 'fsgd')
elif design_input == 'design_mat':
wf.connect(fileList, 'design_mat', rhSBMglmfit, 'design')
wf.connect(fileList, 'contrast_files', rhSBMglmfit, 'contrast')
# perfrom FDR correction if 'FDR' is chosen
if correction_method == 'FDR':
mriFDR = MapNode(FDR(),
iterfield=['in_file1', 'in_file2', 'fdr_sign'],
name='mriFDR')
mriFDR.inputs.fdr = 0.05
mriFDR.inputs.out_thr_file = 'fdr_threshold.txt'
mriFDR.inputs.out_file1 = 'lh.sig_corr.mgh'
mriFDR.inputs.out_file2 = 'rh.sig_corr.mgh'
wf.connect(lhSBMglmfit, 'sig_file', mriFDR, 'in_file1')
wf.connect(lhSBMglmfit, 'mask_file', mriFDR, 'in_mask1')
wf.connect(rhSBMglmfit, 'sig_file', mriFDR, 'in_file2')
wf.connect(rhSBMglmfit, 'mask_file', mriFDR, 'in_mask2')
wf.connect(fileList, ('contrast_sign_files', getElementsFromTxtList),
mriFDR, 'fdr_sign')
# perform Permutation if 'perm' is chosen
elif correction_method == 'perm':
# glmSim = MapNode(GLMFitSim(),
# iterfield=['glm_dir', 'permutation'],
# name='glmSim')
# glmSim.inputs.spaces = '2spaces'
raise NotImplementedError
### Plotting ###
lh_bg_map = op.join(fs_subjects_dir, target_atlas, 'surf', 'lh.sulc')
rh_bg_map = op.join(fs_subjects_dir, target_atlas, 'surf', 'rh.sulc')
# Plot the mean map
plotMeanMaps = MapNode(Function(input_names=['lh_surf', 'lh_surf_map', 'lh_bg_map',
'rh_surf', 'rh_surf_map', 'rh_bg_map',
'out_fname'],
output_name=['out_file'],
function=plot_surf_map),
iterfield=['lh_surf_map', 'rh_surf_map', 'out_fname'],
name='plotMeanMaps')
plotMeanMaps.inputs.lh_bg_map = lh_bg_map
plotMeanMaps.inputs.rh_bg_map = rh_bg_map
plotMeanMaps.inputs.out_fname = ['mean_fwhm{}.png'.format(s) for s in non_zero_fwhm]
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'lh.')),
plotMeanMaps, 'lh_surf')
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'rh.')),
plotMeanMaps, 'rh_surf')
wf.connect(lhSmoothMean, 'out_file', plotMeanMaps, 'lh_surf_map')
wf.connect(rhSmoothMean, 'out_file', plotMeanMaps, 'rh_surf_map')
# Plot uncorrected maps
plot_stat_inputs = ['lh_surf', 'lh_stat_map', 'lh_bg_map',
'rh_surf', 'rh_stat_map', 'rh_bg_map',
'out_fname', 'cmap', 'upper_lim', 'threshold']
plotUncorrectedG = MapNode(Function(input_names=plot_stat_inputs,
output_name=['out_file'],
function=plot_surf_stat),
iterfield=['lh_stat_map', 'rh_stat_map', 'out_fname'],
name='plotUncorrectedG')
plotUncorrectedG.inputs.lh_bg_map = lh_bg_map
plotUncorrectedG.inputs.rh_bg_map = rh_bg_map
plotUncorrectedG.inputs.cmap = 'jet'
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'lh.')),
plotUncorrectedG, 'lh_surf')
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'rh.')),
plotUncorrectedG, 'rh_surf')
wf.connect(fileList, ('contrast_files', makeFStringElementFromFnameList, '.mtx', '_uncorrected_gamma_map.png', True),
plotUncorrectedG, 'out_fname')
wf.connect(lhSBMglmfit, 'gamma_file', plotUncorrectedG, 'lh_stat_map')
wf.connect(rhSBMglmfit, 'gamma_file', plotUncorrectedG, 'rh_stat_map')
plotUncorrectedP = MapNode(Function(input_names=plot_stat_inputs,
output_name=['out_file'],
function=plot_surf_stat),
iterfield=['lh_stat_map', 'rh_stat_map', 'out_fname'],
name='plotUncorrectedP')
plotUncorrectedP.inputs.lh_bg_map = lh_bg_map
plotUncorrectedP.inputs.rh_bg_map = rh_bg_map
plotUncorrectedP.inputs.upper_lim = 10.0
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'lh.')),
plotUncorrectedP, 'lh_surf')
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'rh.')),
plotUncorrectedP, 'rh_surf')
wf.connect(fileList, ('contrast_files', makeFStringElementFromFnameList, '.mtx', '_uncorrected_p_map.png', True),
plotUncorrectedP, 'out_fname')
wf.connect(lhSBMglmfit, 'sig_file', plotUncorrectedP, 'lh_stat_map')
wf.connect(rhSBMglmfit, 'sig_file', plotUncorrectedP, 'rh_stat_map')
# Plot the corrected map
# For gamma first create gamma masked by corrected p
lhMaskGamma = MapNode(MRIsCalc(),
iterfield = ['in_file1', 'in_file2'],
name='lhMaskGamma')
lhMaskGamma.inputs.action = 'masked'
lhMaskGamma.inputs.out_file = 'lh.masked_gamma.mgh'
wf.connect(lhSBMglmfit, 'gamma_file', lhMaskGamma, 'in_file1')
if correction_method == 'FDR':
wf.connect(mriFDR, 'out_file1', lhMaskGamma, 'in_file2')
rhMaskGamma = MapNode(MRIsCalc(),
iterfield = ['in_file1', 'in_file2'],
name='rhMaskGamma')
rhMaskGamma.inputs.action = 'masked'
rhMaskGamma.inputs.out_file = 'rh.masked_gamma.mgh'
wf.connect(rhSBMglmfit, 'gamma_file', rhMaskGamma, 'in_file1')
if correction_method == 'FDR':
wf.connect(mriFDR, 'out_file2', rhMaskGamma, 'in_file2')
# Plot masked gamma
plotCorrectedG = MapNode(Function(input_names=plot_stat_inputs,
output_name=['out_file'],
function=plot_surf_stat),
iterfield=['lh_stat_map', 'rh_stat_map', 'out_fname'],
name='plotCorrectedG')
plotCorrectedG.inputs.lh_bg_map = lh_bg_map
plotCorrectedG.inputs.rh_bg_map = rh_bg_map
plotCorrectedG.inputs.cmap = 'jet'
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'lh.')),
plotCorrectedG, 'lh_surf')
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'rh.')),
plotCorrectedG, 'rh_surf')
wf.connect(fileList, ('contrast_files', makeFStringElementFromFnameList, '.mtx', '_masked_gamma_map.png', True),
plotCorrectedG, 'out_fname')
wf.connect(lhMaskGamma, 'out_file', plotCorrectedG, 'lh_stat_map')
wf.connect(rhMaskGamma, 'out_file', plotCorrectedG, 'rh_stat_map')
# Plot thresholded P
plotCorrectedP = MapNode(Function(input_names=plot_stat_inputs,
output_name=['out_file'],
function=plot_surf_stat),
iterfield=['lh_stat_map', 'rh_stat_map',
'threshold', 'out_fname'],
name='plotCorrectedP')
plotCorrectedP.inputs.lh_bg_map = op.join(fs_subjects_dir, target_atlas, 'surf', 'lh.sulc')
plotCorrectedP.inputs.rh_bg_map = op.join(fs_subjects_dir, target_atlas, 'surf', 'rh.sulc')
plotCorrectedP.inputs.upper_lim = 10.0
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'lh.')),
plotCorrectedP, 'lh_surf')
wf.connect(plotSurfList, ('surf', prependString, op.join(fs_subjects_dir, target_atlas, 'surf', 'rh.')),
plotCorrectedP, 'rh_surf')
wf.connect(lhSBMglmfit, 'sig_file', plotCorrectedP, 'lh_stat_map')
wf.connect(rhSBMglmfit, 'sig_file', plotCorrectedP, 'rh_stat_map')
wf.connect(fileList, ('contrast_files', makeFStringElementFromFnameList, '.mtx', '_corrected_p_map.png', True),
plotCorrectedP, 'out_fname')
if correction_method == 'FDR':
wf.connect(mriFDR, 'out_thr_file', plotCorrectedP, 'threshold')
# # Datasink
# datasink = Node(DataSink(base_directory=base_dir,
# container='%sSink' % name),
# name='Datasink')
#
# glm_outputs = ['gamma_file', 'gamma_var_file', 'sig_file', 'ftest_file']
# for out in glm_outputs:
# wf.connect(lhSBMglmfit, out, datasink, 'lhSBMglm_{}'.format(out))
# wf.connect(rhSBMglmfit, out, datasink, 'rhSBMglm_{}'.format(out))
#
# if correction_method == 'FDR':
# wf.connect(mriFDR, 'out_file1', datasink, 'lhSBM_fdr_corrected_sig')
# wf.connect(mriFDR, 'out_file2', datasink, 'rhSBM_fdr_corrected_sig')
#
# wf.connect(lhMaskGamma, 'out_file', datasink, 'lhSBM_masked_gamma')
# wf.connect(rhMaskGamma, 'out_file', datasink, 'rhSBM_masked_gamma')
#
# wf.connect(plotMeanMaps, 'out_file', datasink, 'mean_map_png')
# wf.connect(plotUncorrectedG, 'out_file', datasink, 'uncorrected_gamma_png')
# wf.connect(plotUncorrectedP, 'out_file', datasink, 'uncorrected_p_png')
# wf.connect(plotCorrectedG, 'out_file', datasink, 'masked_gamma_png')
# wf.connect(plotCorrectedP, 'out_file', datasink, 'corrected_p_png')
#
return wf