def QA_workflow(name='QA'):
""" Workflow that generates a Quality Assurance Report
Parameters
----------
name : name of workflow
Inputs
------
inputspec.subject_id :
inputspec.config_params :
inputspec.in_file :
inputspec.art_file :
inputspec.motion_plots :
inputspec.reg_file :
inputspec.tsnr_detrended :
inputspec.tsnr :
inputspec.tsnr_mean :
inputspec.tsnr_stddev :
inputspec.ADnorm :
inputspec.TR :
inputspec.sd : freesurfer subjects directory
"""
# Define Workflow
workflow =pe.Workflow(name=name)
inputspec = pe.Node(interface=util.IdentityInterface(fields=['subject_id',
'config_params',
'in_file',
'art_file',
'motion_plots',
'reg_file',
'tsnr',
'tsnr_mean',
'tsnr_stddev',
'ADnorm',
'TR',
'sd']),
name='inputspec')
infosource = pe.Node(util.IdentityInterface(fields=['subject_id']),
name='subject_names')
infosource.iterables = ('subject_id', c.subjects)
datagrabber = preproc_datagrabber()
datagrabber.inputs.fwhm = c.fwhm
orig_datagrabber = c.create_dataflow()
workflow.connect(infosource, 'subject_id',
datagrabber, 'subject_id')
workflow.connect(infosource, 'subject_id', orig_datagrabber, 'subject_id')
workflow.connect(orig_datagrabber, 'func', inputspec, 'in_file')
workflow.connect(infosource, 'subject_id', inputspec, 'subject_id')
workflow.connect(datagrabber, 'outlier_files', inputspec, 'art_file')
#workflow.connect(datagrabber, 'motion_plots', inputspec, 'motion_plots')
workflow.connect(datagrabber, 'reg_file', inputspec, 'reg_file')
workflow.connect(datagrabber, 'tsnr', inputspec, 'tsnr')
workflow.connect(datagrabber, 'tsnr_stddev', inputspec, 'tsnr_stddev')
workflow.connect(datagrabber, 'art_norm', inputspec, 'ADnorm')
inputspec.inputs.TR = c.TR
inputspec.inputs.sd = c.surf_dir
# Define Nodes
plot_m = pe.MapNode(util.Function(input_names=['motion_parameters'],
output_names=['fname'],
function=plot_motion),
name="motion_plots",
iterfield=['motion_parameters'])
workflow.connect(datagrabber,'motion_parameters',plot_m,'motion_parameters')
workflow.connect(plot_m, 'fname',inputspec,'motion_plots')
tsdiff = pe.MapNode(util.Function(input_names = ['img'],
output_names = ['out_file'],
function=tsdiffana),
name='tsdiffana', iterfield=["img"])
art_info = pe.MapNode(util.Function(input_names = ['art_file'],
output_names = ['table','out'],
function=art_output),
name='art_output', iterfield=["art_file"])
fssource = pe.Node(interface = FreeSurferSource(),name='fssource')
plotribbon = pe.Node(util.Function(input_names=['Brain'],
output_names=['images'],
function=plot_ribbon),
name="plot_ribbon")
workflow.connect(fssource, 'ribbon', plotribbon, 'Brain')
plotanat = pe.Node(util.Function(input_names=['brain'],
output_names=['images'],
function=plot_anat),
name="plot_anat")
roidevplot = tsnr_roi(plot=False,name='tsnr_stddev_roi',roi=['all'])
roidevplot.inputs.inputspec.TR = c.TR
roisnrplot = tsnr_roi(plot=False,name='SNR_roi',roi=['all'])
roisnrplot.inputs.inputspec.TR = c.TR
workflow.connect(fssource, ('aparc_aseg', pickfirst), roisnrplot, 'inputspec.aparc_aseg')
workflow.connect(fssource, ('aparc_aseg', pickfirst), roidevplot, 'inputspec.aparc_aseg')
workflow.connect(infosource, 'subject_id', roidevplot, 'inputspec.subject')
workflow.connect(infosource, 'subject_id', roisnrplot, 'inputspec.subject')
tablecombine = pe.MapNode(util.Function(input_names = ['roidev',
'roisnr'],
output_names = ['roisnr'],
function = combine_table),
name='combinetable', iterfield=['roidev','roisnr'])
adnormplot = pe.MapNode(util.Function(input_names = ['ADnorm','TR','norm_thresh','out'],
output_names = ['plot'],
function=plot_ADnorm),
name='ADnormplot', iterfield=['ADnorm','out'])
adnormplot.inputs.norm_thresh = c.norm_thresh
workflow.connect(art_info,'out',adnormplot,'out')
convert = pe.Node(interface=fs.MRIConvert(),name='converter')
voltransform = pe.MapNode(interface=ApplyVolTransform(),name='register',iterfield=['source_file'])
overlaynew = pe.MapNode(util.Function(input_names=['stat_image','background_image','threshold',"dB"],
output_names=['fnames'], function=overlay_dB),
name='overlay_new', iterfield=['stat_image'])
overlaynew.inputs.dB = False
overlaynew.inputs.threshold = 20
overlaymask = pe.Node(util.Function(input_names=['stat_image','background_image','threshold'],
output_names=['fnames'], function=overlay_new),
name='overlay_mask')
overlaymask.inputs.threshold = 0
#workflow.connect(datagrabber, 'mask', overlaymask, 'background_image')
workflow.connect(datagrabber, 'mean_image', plotanat, 'brain')
#workflow.connect(overlaymask,'out_file', slicermask, 'in_file')
write_rep = pe.Node(interface=ReportSink(orderfields=['Introduction',
'in_file',
'config_params',
'Art_Detect',
'Mean_Functional',
'Ribbon',
'motion_plots',
'tsdiffana',
'ADnorm',
'TSNR_Images',
'tsnr_roi_table']),
name='report_sink')
write_rep.inputs.Introduction = "Quality Assurance Report for fMRI preprocessing."
write_rep.inputs.base_directory = os.path.join(c.sink_dir,'analyses','func')
write_rep.inputs.report_name = "Preprocessing_Report"
write_rep.inputs.json_sink = c.json_sink
workflow.connect(infosource,'subject_id',write_rep,'container')
workflow.connect(plotanat, 'images', write_rep, "Mean_Functional")
#workflow.connect(slicermask,'out_file', write_rep, "Brain_Mask_and_Mean_Functional")
# Define Inputs
convert.inputs.out_type = 'niigz'
convert.inputs.in_type = 'mgz'
# Define Connections
workflow.connect(inputspec,'TR',adnormplot,'TR')
workflow.connect(inputspec,'subject_id',fssource,'subject_id')
workflow.connect(inputspec,'sd',fssource,'subjects_dir')
workflow.connect(inputspec,'in_file',write_rep,'in_file')
workflow.connect(inputspec,'art_file',art_info,'art_file')
workflow.connect(art_info,('table',to1table), write_rep,'Art_Detect')
workflow.connect(inputspec,'motion_plots',write_rep,'motion_plots')
workflow.connect(inputspec,'in_file',tsdiff,'img')
workflow.connect(tsdiff,"out_file",write_rep,"tsdiffana")
workflow.connect(inputspec,('config_params',totable), write_rep,'config_params')
workflow.connect(inputspec,'reg_file',roidevplot,'inputspec.reg_file')
workflow.connect(inputspec,'tsnr_stddev',roidevplot,'inputspec.tsnr_file')
workflow.connect(roidevplot,'outputspec.roi_table',tablecombine,'roidev')
workflow.connect(inputspec,'reg_file',roisnrplot,'inputspec.reg_file')
workflow.connect(inputspec,'tsnr',roisnrplot,'inputspec.tsnr_file')
workflow.connect(roisnrplot,'outputspec.roi_table',tablecombine,'roisnr')
workflow.connect(tablecombine, ('roisnr',to1table), write_rep, 'tsnr_roi_table')
workflow.connect(inputspec,'ADnorm',adnormplot,'ADnorm')
workflow.connect(adnormplot,'plot',write_rep,'ADnorm')
workflow.connect(fssource,'orig',convert,'in_file')
workflow.connect(convert,'out_file',voltransform,'target_file')
workflow.connect(inputspec,'reg_file',voltransform,'reg_file')
workflow.connect(inputspec,'tsnr',voltransform, 'source_file')
workflow.connect(plotribbon, 'images', write_rep, 'Ribbon')
workflow.connect(voltransform,'transformed_file', overlaynew,'stat_image')
workflow.connect(convert,'out_file', overlaynew,'background_image')
workflow.connect(overlaynew, 'fnames', write_rep, 'TSNR_Images')
workflow.write_graph()
return workflow
