def create_prep(name='preproc'):
""" Base preprocessing workflow for task and resting state fMRI
Parameters
----------
name : name of workflow. Default = 'preproc'
Inputs
------
inputspec.fssubject_id :
inputspec.fssubject_dir :
inputspec.func :
inputspec.highpass :
inputspec.num_noise_components :
inputspec.ad_normthresh :
inputspec.ad_zthresh :
inputspec.tr :
inputspec.interleaved :
inputspec.sliceorder :
inputspec.compcor_select :
inputspec.highpass_sigma :
inputspec.lowpass_sigma :
inputspec.reg_params :
inputspec.FM_TEdiff :
inputspec.FM_Echo_spacing :
inputspec.FM_sigma :
Outputs
-------
outputspec.reference :
outputspec.motion_parameters :
outputspec.realigned_files :
outputspec.mask :
outputspec.smoothed_files :
outputspec.highpassed_files :
outputspec.mean :
outputspec.combined_motion :
outputspec.outlier_files :
outputspec.mask :
outputspec.reg_cost :
outputspec.reg_file :
outputspec.noise_components :
outputspec.tsnr_file :
outputspec.stddev_file :
outputspec.filter_file :
outputspec.scaled_files :
outputspec.z_img :
outputspec.motion_plots :
outputspec.FM_unwarped_mean :
outputspec.FM_unwarped_epi :
Returns
-------
workflow : preprocessing workflow
"""
import nipype.interfaces.fsl as fsl # fsl
import nipype.algorithms.rapidart as ra # rapid artifact detection
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
from modular_nodes import create_mod_smooth, mod_realign, mod_despike
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
preproc = pe.Workflow(name=name)
# Compcorr node
compcor = create_compcorr()
# Input node
inputnode = pe.Node(util.IdentityInterface(fields=['fssubject_id',
'fssubject_dir',
'func',
'highpass',
'num_noise_components',
'ad_normthresh',
'ad_zthresh',
'tr',
'do_slicetime',
'sliceorder',
'compcor_select',
'highpass_freq',
'lowpass_freq',
'reg_params',
'FM_TEdiff',
'FM_Echo_spacing',
'FM_sigma',
'motion_correct_node',
'smooth_type',
'surface_fwhm',
'filter_type',
'timepoints_to_remove',
'do_whitening',
'regress_before_PCA',
'realign_parameters',
'do_despike',
'anatomical']),
name='inputspec')
# Separate input node for FWHM
inputnode_fwhm = pe.Node(util.IdentityInterface(fields=['fwhm']),
name='fwhm_input')
# strip ids
strip_rois = pe.MapNode(fsl.ExtractROI(),name='extractroi',iterfield='in_file')
strip_rois.inputs.t_size = -1
preproc.connect(inputnode,'timepoints_to_remove',strip_rois,'t_min')
# convert BOLD images to float
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
#afni despike
despike=pe.MapNode(util.Function(input_names=['in_file',"do_despike"],
output_names=["out_file"],
function=mod_despike),
name="despike",iterfield=["in_file"])
preproc.connect(inputnode,"do_despike",despike,"do_despike")
# define the motion correction node
#motion_correct = pe.Node(interface=FmriRealign4d(),
# name='realign')
motion_correct = pe.Node(util.Function(input_names=['node','in_file','tr',
'do_slicetime','sliceorder',"parameters"],
output_names=['out_file','par_file','parameter_source'],
function=mod_realign),
name="mod_realign")
preproc.connect(inputnode,'motion_correct_node',
motion_correct, 'node')
# construct motion plots
#plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
# name='plot_motion',
# iterfield=['in_file'])
# rapidArt for artifactual timepoint detection
ad = pe.Node(ra.ArtifactDetect(save_plot=False),
name='artifactdetect')
# extract the mean volume if the first functional run
meanfunc = art_mean_workflow()
# generate a freesurfer workflow that will return the mask
getmask = create_getmask_flow()
# create a SUSAN smoothing workflow, and smooth each run with
# 75% of the median value for each run as the brightness
# threshold.
smooth = create_mod_smooth(name="modular_smooth",
separate_masks=False)
preproc.connect(inputnode,'smooth_type', smooth,'inputnode.smooth_type')
# choose susan function
"""
The following node selects smooth or unsmoothed data
depending on the fwhm. This is because SUSAN defaults
to smoothing the data with about the voxel size of
the input data if the fwhm parameter is less than 1/3 of
the voxel size.
"""
choosesusan = pe.Node(util.Function(input_names=['fwhm',
'motion_files',
'smoothed_files'],
output_names=['cor_smoothed_files'],
function=choose_susan),
name='select_smooth')
# scale the median value of each run to 10,000
meanscale = pe.MapNode(interface=fsl.ImageMaths(suffix='_gms'),
iterfield=['in_file',
'op_string'],
name='scale_median')
# determine the median value of the MASKED functional runs
medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
iterfield=['in_file'],
name='compute_median_val')
# temporal highpass filtering
highpass = pe.MapNode(interface=fsl.ImageMaths(suffix='_tempfilt'),
iterfield=['in_file'],
name='highpass')
# Calculate the z-score of output
zscore = pe.MapNode(interface=util.Function(input_names=['image','outliers'],
output_names=['z_img'],
function=z_image),
name='z_score',
iterfield=['image','outliers'])
# declare some node inputs...
#plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
#ad.inputs.parameter_source = 'FSL'
meanfunc.inputs.inputspec.parameter_source = 'FSL'
ad.inputs.mask_type = 'file'
ad.inputs.use_differences = [True, False]
getmask.inputs.inputspec.contrast_type = 't2'
getmask.inputs.register.out_fsl_file = True
fssource = getmask.get_node('fssource')
# make connections...
preproc.connect(inputnode, 'fssubject_id',
getmask, 'inputspec.subject_id')
preproc.connect(inputnode, 'ad_normthresh',
ad, 'norm_threshold')
preproc.connect(inputnode, 'ad_zthresh',
ad, 'zintensity_threshold')
preproc.connect(inputnode, 'tr',
motion_correct, 'tr')
preproc.connect(inputnode, 'realign_parameters',
motion_correct, 'parameters')
preproc.connect(motion_correct,'parameter_source',
ad,'parameter_source')
preproc.connect(inputnode, 'do_slicetime',
motion_correct, 'do_slicetime')
preproc.connect(inputnode, 'sliceorder',
motion_correct, 'sliceorder')
preproc.connect(inputnode, 'compcor_select',
compcor, 'inputspec.selector')
preproc.connect(inputnode, 'fssubject_dir',
getmask, 'inputspec.subjects_dir')
#preproc.connect(inputnode, 'func',
# img2float, 'in_file')
preproc.connect(inputnode, 'func', strip_rois, 'in_file')
preproc.connect(strip_rois, 'roi_file', img2float, 'in_file')
preproc.connect(img2float, 'out_file', despike, "in_file")
preproc.connect(despike,"out_file", motion_correct, 'in_file')
#preproc.connect(motion_correct, 'par_file',
# plot_motion, 'in_file')
preproc.connect(motion_correct, 'out_file',
meanfunc, 'inputspec.realigned_files')
preproc.connect(motion_correct, 'par_file',
meanfunc, 'inputspec.realignment_parameters')
preproc.connect(meanfunc, 'outputspec.mean_image',
getmask, 'inputspec.source_file')
preproc.connect(inputnode, 'num_noise_components',
compcor, 'inputspec.num_components')
preproc.connect(inputnode, 'regress_before_PCA',
compcor, 'inputspec.regress_before_PCA')
preproc.connect(motion_correct, 'out_file',
compcor, 'inputspec.realigned_file')
preproc.connect(meanfunc, 'outputspec.mean_image',
compcor, 'inputspec.mean_file')
preproc.connect(fssource, 'aseg',
compcor, 'inputspec.fsaseg_file')
preproc.connect(getmask, ('outputspec.reg_file', pickfirst),
compcor, 'inputspec.reg_file')
preproc.connect(ad, 'outlier_files',
compcor, 'inputspec.outlier_files')
preproc.connect(motion_correct, 'par_file',
compcor, 'inputspec.realignment_parameters')
preproc.connect(motion_correct, 'out_file',
ad, 'realigned_files')
preproc.connect(motion_correct, 'par_file',
ad, 'realignment_parameters')
preproc.connect(getmask, ('outputspec.mask_file', pickfirst),
ad, 'mask_file')
preproc.connect(getmask, ('outputspec.mask_file', pickfirst),
medianval, 'mask_file')
preproc.connect(inputnode_fwhm, 'fwhm',
smooth, 'inputnode.fwhm')
preproc.connect(motion_correct, 'out_file',
smooth, 'inputnode.in_files')
preproc.connect(getmask, ('outputspec.mask_file',pickfirst),
smooth, 'inputnode.mask_file')
preproc.connect(getmask, ('outputspec.reg_file', pickfirst),
smooth, 'inputnode.reg_file')
preproc.connect(inputnode,'surface_fwhm',
smooth, 'inputnode.surface_fwhm')
preproc.connect(inputnode, 'fssubject_dir',
smooth, 'inputnode.surf_dir')
preproc.connect(smooth, 'outputnode.smoothed_files',
choosesusan, 'smoothed_files')
preproc.connect(motion_correct, 'out_file',
choosesusan, 'motion_files')
preproc.connect(inputnode_fwhm, 'fwhm',
choosesusan, 'fwhm')
preproc.connect(choosesusan, 'cor_smoothed_files',
meanscale, 'in_file')
preproc.connect(choosesusan, 'cor_smoothed_files',
medianval, 'in_file')
preproc.connect(medianval, ('out_stat', getmeanscale),
meanscale, 'op_string')
preproc.connect(inputnode, ('highpass', highpass_operand),
highpass, 'op_string')
preproc.connect(meanscale, 'out_file',
highpass, 'in_file')
preproc.connect(highpass, 'out_file',
zscore, 'image')
preproc.connect(ad, 'outlier_files',
zscore, 'outliers')
# create output node
outputnode = pe.Node(interface=util.IdentityInterface(
fields=['mean',
'motion_parameters',
'realigned_files',
'smoothed_files',
'highpassed_files',
'combined_motion',
'outlier_files',
'outlier_stat_files',
'mask',
'reg_cost',
'reg_file',
'reg_fsl_file',
'noise_components',
'tsnr_file',
'stddev_file',
'tsnr_detrended',
'filter_file',
'scaled_files','unmasked_fullspectrum',
'z_img',
'motion_plots',
'FM_unwarped_epi',
'FM_unwarped_mean',
'vsm_file',
'bandpassed_file',
'intensity_files',
'noise_mask',
'csf_mask']),
name='outputspec')
# make output connection
preproc.connect(meanfunc, 'outputspec.mean_image',
outputnode, 'mean')
preproc.connect(motion_correct, 'par_file',
outputnode, 'motion_parameters')
preproc.connect(motion_correct, 'out_file',
outputnode, 'realigned_files')
preproc.connect(highpass, 'out_file',
outputnode, 'highpassed_files')
preproc.connect(ad, 'norm_files',
outputnode, 'combined_motion')
preproc.connect(ad, 'outlier_files',
outputnode, 'outlier_files')
preproc.connect(ad, 'intensity_files',
outputnode, 'intensity_files')
preproc.connect(ad, 'statistic_files',
outputnode, 'outlier_stat_files')
preproc.connect(compcor, 'outputspec.noise_components',
outputnode, 'noise_components')
preproc.connect(compcor, 'outputspec.noise_mask',
outputnode, 'noise_mask')
preproc.connect(compcor, 'outputspec.csf_mask',
outputnode, 'csf_mask')
preproc.connect(getmask, 'outputspec.mask_file',
outputnode, 'mask')
preproc.connect(getmask, 'register.out_fsl_file',
outputnode, 'reg_fsl_file')
preproc.connect(getmask, 'outputspec.reg_file',
outputnode, 'reg_file')
preproc.connect(getmask, 'outputspec.reg_cost',
outputnode, 'reg_cost')
preproc.connect(choosesusan, 'cor_smoothed_files',
outputnode, 'smoothed_files')
preproc.connect(compcor, 'outputspec.tsnr_file',
outputnode, 'tsnr_file')
preproc.connect(compcor, 'outputspec.stddev_file',
outputnode, 'stddev_file')
preproc.connect(compcor, 'outputspec.tsnr_detrended',
outputnode, 'tsnr_detrended')
preproc.connect(zscore,'z_img',
outputnode,'z_img')
#preproc.connect(plot_motion,'out_file',
# outputnode,'motion_plots')
return preproc
def create_prep(name='preproc'):
""" Base preprocessing workflow for task and resting state fMRI
Parameters
----------
name : name of workflow. Default = 'preproc'
Inputs
------
inputspec.fssubject_id :
inputspec.fssubject_dir :
inputspec.func :
inputspec.highpass :
inputspec.num_noise_components :
inputspec.ad_normthresh :
inputspec.ad_zthresh :
inputspec.tr :
inputspec.interleaved :
inputspec.sliceorder :
inputspec.compcor_select :
inputspec.highpass_sigma :
inputspec.lowpass_sigma :
inputspec.reg_params :
inputspec.FM_TEdiff :
inputspec.FM_Echo_spacing :
inputspec.FM_sigma :
Outputs
-------
outputspec.reference :
outputspec.motion_parameters :
outputspec.realigned_files :
outputspec.mask :
outputspec.smoothed_files :
outputspec.highpassed_files :
outputspec.mean :
outputspec.combined_motion :
outputspec.outlier_files :
outputspec.mask :
outputspec.reg_cost :
outputspec.reg_file :
outputspec.noise_components :
outputspec.tsnr_file :
outputspec.stddev_file :
outputspec.filter_file :
outputspec.scaled_files :
outputspec.z_img :
outputspec.motion_plots :
outputspec.FM_unwarped_mean :
outputspec.FM_unwarped_epi :
Returns
-------
workflow : preprocessing workflow
"""
import nipype.interfaces.fsl as fsl # fsl
import nipype.algorithms.rapidart as ra # rapid artifact detection
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
from modular_nodes import create_mod_smooth, mod_realign, mod_despike
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
preproc = pe.Workflow(name=name)
# Compcorr node
compcor = create_compcorr()
# Input node
inputnode = pe.Node(util.IdentityInterface(fields=[
'fssubject_id', 'fssubject_dir', 'func', 'highpass',
'num_noise_components', 'ad_normthresh', 'ad_zthresh', 'tr',
'do_slicetime', 'sliceorder', 'compcor_select', 'highpass_freq',
'lowpass_freq', 'reg_params', 'FM_TEdiff', 'FM_Echo_spacing',
'FM_sigma', 'motion_correct_node', 'smooth_type', 'surface_fwhm',
'filter_type', 'timepoints_to_remove', 'do_whitening',
'regress_before_PCA', 'realign_parameters', 'do_despike', 'anatomical'
]),
name='inputspec')
# Separate input node for FWHM
inputnode_fwhm = pe.Node(util.IdentityInterface(fields=['fwhm']),
name='fwhm_input')
# strip ids
strip_rois = pe.MapNode(fsl.ExtractROI(),
name='extractroi',
iterfield='in_file')
strip_rois.inputs.t_size = -1
preproc.connect(inputnode, 'timepoints_to_remove', strip_rois, 't_min')
# convert BOLD images to float
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
#afni despike
despike = pe.MapNode(util.Function(input_names=['in_file', "do_despike"],
output_names=["out_file"],
function=mod_despike),
name="despike",
iterfield=["in_file"])
preproc.connect(inputnode, "do_despike", despike, "do_despike")
# define the motion correction node
#motion_correct = pe.Node(interface=FmriRealign4d(),
# name='realign')
motion_correct = pe.Node(util.Function(
input_names=[
'node', 'in_file', 'tr', 'do_slicetime', 'sliceorder', "parameters"
],
output_names=['out_file', 'par_file', 'parameter_source'],
function=mod_realign),
name="mod_realign")
preproc.connect(inputnode, 'motion_correct_node', motion_correct, 'node')
# construct motion plots
#plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
# name='plot_motion',
# iterfield=['in_file'])
# rapidArt for artifactual timepoint detection
ad = pe.Node(ra.ArtifactDetect(save_plot=False), name='artifactdetect')
# extract the mean volume if the first functional run
meanfunc = art_mean_workflow()
# generate a freesurfer workflow that will return the mask
getmask = create_getmask_flow()
# create a SUSAN smoothing workflow, and smooth each run with
# 75% of the median value for each run as the brightness
# threshold.
smooth = create_mod_smooth(name="modular_smooth", separate_masks=False)
preproc.connect(inputnode, 'smooth_type', smooth, 'inputnode.smooth_type')
# choose susan function
"""
The following node selects smooth or unsmoothed data
depending on the fwhm. This is because SUSAN defaults
to smoothing the data with about the voxel size of
the input data if the fwhm parameter is less than 1/3 of
the voxel size.
"""
choosesusan = pe.Node(util.Function(
input_names=['fwhm', 'motion_files', 'smoothed_files'],
output_names=['cor_smoothed_files'],
function=choose_susan),
name='select_smooth')
# scale the median value of each run to 10,000
meanscale = pe.MapNode(interface=fsl.ImageMaths(suffix='_gms'),
iterfield=['in_file', 'op_string'],
name='scale_median')
# determine the median value of the MASKED functional runs
medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
iterfield=['in_file'],
name='compute_median_val')
# temporal highpass filtering
highpass = pe.MapNode(interface=fsl.ImageMaths(suffix='_tempfilt'),
iterfield=['in_file'],
name='highpass')
# Calculate the z-score of output
zscore = pe.MapNode(interface=util.Function(
input_names=['image', 'outliers'],
output_names=['z_img'],
function=z_image),
name='z_score',
iterfield=['image', 'outliers'])
# declare some node inputs...
#plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
#ad.inputs.parameter_source = 'FSL'
meanfunc.inputs.inputspec.parameter_source = 'FSL'
ad.inputs.mask_type = 'file'
ad.inputs.use_differences = [True, False]
getmask.inputs.inputspec.contrast_type = 't2'
getmask.inputs.register.out_fsl_file = True
fssource = getmask.get_node('fssource')
# make connections...
preproc.connect(inputnode, 'fssubject_id', getmask, 'inputspec.subject_id')
preproc.connect(inputnode, 'ad_normthresh', ad, 'norm_threshold')
preproc.connect(inputnode, 'ad_zthresh', ad, 'zintensity_threshold')
preproc.connect(inputnode, 'tr', motion_correct, 'tr')
preproc.connect(inputnode, 'realign_parameters', motion_correct,
'parameters')
preproc.connect(motion_correct, 'parameter_source', ad, 'parameter_source')
preproc.connect(inputnode, 'do_slicetime', motion_correct, 'do_slicetime')
preproc.connect(inputnode, 'sliceorder', motion_correct, 'sliceorder')
preproc.connect(inputnode, 'compcor_select', compcor, 'inputspec.selector')
preproc.connect(inputnode, 'fssubject_dir', getmask,
'inputspec.subjects_dir')
#preproc.connect(inputnode, 'func',
# img2float, 'in_file')
preproc.connect(inputnode, 'func', strip_rois, 'in_file')
preproc.connect(strip_rois, 'roi_file', img2float, 'in_file')
preproc.connect(img2float, 'out_file', despike, "in_file")
preproc.connect(despike, "out_file", motion_correct, 'in_file')
#preproc.connect(motion_correct, 'par_file',
# plot_motion, 'in_file')
preproc.connect(motion_correct, 'out_file', meanfunc,
'inputspec.realigned_files')
preproc.connect(motion_correct, 'par_file', meanfunc,
'inputspec.realignment_parameters')
preproc.connect(meanfunc, 'outputspec.mean_image', getmask,
'inputspec.source_file')
preproc.connect(inputnode, 'num_noise_components', compcor,
'inputspec.num_components')
preproc.connect(inputnode, 'regress_before_PCA', compcor,
'inputspec.regress_before_PCA')
preproc.connect(motion_correct, 'out_file', compcor,
'inputspec.realigned_file')
preproc.connect(meanfunc, 'outputspec.mean_image', compcor,
'inputspec.mean_file')
preproc.connect(fssource, 'aseg', compcor, 'inputspec.fsaseg_file')
preproc.connect(getmask, ('outputspec.reg_file', pickfirst), compcor,
'inputspec.reg_file')
preproc.connect(ad, 'outlier_files', compcor, 'inputspec.outlier_files')
preproc.connect(motion_correct, 'par_file', compcor,
'inputspec.realignment_parameters')
preproc.connect(motion_correct, 'out_file', ad, 'realigned_files')
preproc.connect(motion_correct, 'par_file', ad, 'realignment_parameters')
preproc.connect(getmask, ('outputspec.mask_file', pickfirst), ad,
'mask_file')
preproc.connect(getmask, ('outputspec.mask_file', pickfirst), medianval,
'mask_file')
preproc.connect(inputnode_fwhm, 'fwhm', smooth, 'inputnode.fwhm')
preproc.connect(motion_correct, 'out_file', smooth, 'inputnode.in_files')
preproc.connect(getmask, ('outputspec.mask_file', pickfirst), smooth,
'inputnode.mask_file')
preproc.connect(getmask, ('outputspec.reg_file', pickfirst), smooth,
'inputnode.reg_file')
preproc.connect(inputnode, 'surface_fwhm', smooth,
'inputnode.surface_fwhm')
preproc.connect(inputnode, 'fssubject_dir', smooth, 'inputnode.surf_dir')
preproc.connect(smooth, 'outputnode.smoothed_files', choosesusan,
'smoothed_files')
preproc.connect(motion_correct, 'out_file', choosesusan, 'motion_files')
preproc.connect(inputnode_fwhm, 'fwhm', choosesusan, 'fwhm')
preproc.connect(choosesusan, 'cor_smoothed_files', meanscale, 'in_file')
preproc.connect(choosesusan, 'cor_smoothed_files', medianval, 'in_file')
preproc.connect(medianval, ('out_stat', getmeanscale), meanscale,
'op_string')
preproc.connect(inputnode, ('highpass', highpass_operand), highpass,
'op_string')
preproc.connect(meanscale, 'out_file', highpass, 'in_file')
preproc.connect(highpass, 'out_file', zscore, 'image')
preproc.connect(ad, 'outlier_files', zscore, 'outliers')
# create output node
outputnode = pe.Node(interface=util.IdentityInterface(fields=[
'mean', 'motion_parameters', 'realigned_files', 'smoothed_files',
'highpassed_files', 'combined_motion', 'outlier_files',
'outlier_stat_files', 'mask', 'reg_cost', 'reg_file', 'reg_fsl_file',
'noise_components', 'tsnr_file', 'stddev_file', 'tsnr_detrended',
'filter_file', 'scaled_files', 'unmasked_fullspectrum', 'z_img',
'motion_plots', 'FM_unwarped_epi', 'FM_unwarped_mean', 'vsm_file',
'bandpassed_file', 'intensity_files', 'noise_mask', 'csf_mask'
]),
name='outputspec')
# make output connection
preproc.connect(meanfunc, 'outputspec.mean_image', outputnode, 'mean')
preproc.connect(motion_correct, 'par_file', outputnode,
'motion_parameters')
preproc.connect(motion_correct, 'out_file', outputnode, 'realigned_files')
preproc.connect(highpass, 'out_file', outputnode, 'highpassed_files')
preproc.connect(ad, 'norm_files', outputnode, 'combined_motion')
preproc.connect(ad, 'outlier_files', outputnode, 'outlier_files')
preproc.connect(ad, 'intensity_files', outputnode, 'intensity_files')
preproc.connect(ad, 'statistic_files', outputnode, 'outlier_stat_files')
preproc.connect(compcor, 'outputspec.noise_components', outputnode,
'noise_components')
preproc.connect(compcor, 'outputspec.noise_mask', outputnode, 'noise_mask')
preproc.connect(compcor, 'outputspec.csf_mask', outputnode, 'csf_mask')
preproc.connect(getmask, 'outputspec.mask_file', outputnode, 'mask')
preproc.connect(getmask, 'register.out_fsl_file', outputnode,
'reg_fsl_file')
preproc.connect(getmask, 'outputspec.reg_file', outputnode, 'reg_file')
preproc.connect(getmask, 'outputspec.reg_cost', outputnode, 'reg_cost')
preproc.connect(choosesusan, 'cor_smoothed_files', outputnode,
'smoothed_files')
preproc.connect(compcor, 'outputspec.tsnr_file', outputnode, 'tsnr_file')
preproc.connect(compcor, 'outputspec.stddev_file', outputnode,
'stddev_file')
preproc.connect(compcor, 'outputspec.tsnr_detrended', outputnode,
'tsnr_detrended')
preproc.connect(zscore, 'z_img', outputnode, 'z_img')
#preproc.connect(plot_motion,'out_file',
# outputnode,'motion_plots')
return preproc
def create_spm_preproc(c, name='preproc'):
"""Create an spm preprocessing workflow with freesurfer registration and
artifact detection.
The workflow realigns and smooths and registers the functional images with
the subject's freesurfer space.
Example
-------
>>> preproc = create_spm_preproc()
>>> preproc.base_dir = '.'
>>> preproc.inputs.inputspec.fwhm = 6
>>> preproc.inputs.inputspec.subject_id = 's1'
>>> preproc.inputs.inputspec.subjects_dir = '.'
>>> preproc.inputs.inputspec.functionals = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.norm_threshold = 1
>>> preproc.inputs.inputspec.zintensity_threshold = 3
Inputs::
inputspec.functionals : functional runs use 4d nifti
inputspec.subject_id : freesurfer subject id
inputspec.subjects_dir : freesurfer subjects dir
inputspec.fwhm : smoothing fwhm
inputspec.norm_threshold : norm threshold for outliers
inputspec.zintensity_threshold : intensity threshold in z-score
Outputs::
outputspec.realignment_parameters : realignment parameter files
outputspec.smoothed_files : smoothed functional files
outputspec.outlier_files : list of outliers
outputspec.outlier_stats : statistics of outliers
outputspec.outlier_plots : images of outliers
outputspec.mask_file : binary mask file in reference image space
outputspec.reg_file : registration file that maps reference image to
freesurfer space
outputspec.reg_cost : cost of registration (useful for detecting misalignment)
"""
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
import nipype.algorithms.rapidart as ra
import nipype.interfaces.spm as spm
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
"""
Initialize the workflow
"""
workflow = pe.Workflow(name=name)
"""
Define the inputs to this workflow
"""
inputnode = pe.Node(niu.IdentityInterface(fields=[
'functionals', 'subject_id', 'subjects_dir', 'fwhm', 'norm_threshold',
'zintensity_threshold', 'tr', 'do_slicetime', 'sliceorder', 'node',
'csf_prob', 'wm_prob', 'gm_prob'
]),
name='inputspec')
"""
Setup the processing nodes and create the mask generation and coregistration
workflow
"""
poplist = lambda x: x.pop()
#realign = pe.Node(spm.Realign(), name='realign')
sym_func = pe.Node(niu.Function(input_names=['in_file'],
output_names=['out_link'],
function=do_symlink),
name='func_symlink')
realign = pe.Node(niu.Function(
input_names=['node', 'in_file', 'tr', 'do_slicetime', 'sliceorder'],
output_names=['out_file', 'par_file'],
function=mod_realign),
name="mod_realign")
mean = art_mean_workflow()
workflow.connect(realign, 'out_file', mean, 'inputspec.realigned_files')
workflow.connect(realign, 'par_file', mean,
'inputspec.realignment_parameters')
mean.inputs.inputspec.parameter_source = 'FSL' # Modular realign puts it in FSL format for consistency
#workflow.connect(inputnode, 'functionals', realign, 'in_file')
workflow.connect(inputnode, 'functionals', sym_func, 'in_file')
workflow.connect(sym_func, 'out_link', realign, 'in_file')
workflow.connect(inputnode, 'tr', realign, 'tr')
workflow.connect(inputnode, 'do_slicetime', realign, 'do_slicetime')
workflow.connect(inputnode, 'sliceorder', realign, 'sliceorder')
workflow.connect(inputnode, 'node', realign, 'node')
maskflow = create_getmask_flow()
workflow.connect([(inputnode, maskflow,
[('subject_id', 'inputspec.subject_id'),
('subjects_dir', 'inputspec.subjects_dir')])])
maskflow.inputs.inputspec.contrast_type = 't2'
workflow.connect(mean, 'outputspec.mean_image', maskflow,
'inputspec.source_file')
smooth = pe.Node(spm.Smooth(), name='smooth')
normalize = pe.Node(spm.Normalize(jobtype='write'), name='normalize')
normalize_struct = normalize.clone('normalize_struct')
segment = pe.Node(spm.Segment(csf_output_type=[True, True, False],
gm_output_type=[True, True, False],
wm_output_type=[True, True, False]),
name='segment')
mergefunc = lambda in1, in2, in3: [in1, in2, in3]
# merge = pe.Node(niu.Merge(),name='merge')
merge = pe.Node(niu.Function(input_names=['in1', 'in2', 'in3'],
output_names=['out'],
function=mergefunc),
name='merge')
workflow.connect(inputnode, 'csf_prob', merge, 'in3')
workflow.connect(inputnode, 'wm_prob', merge, 'in2')
workflow.connect(inputnode, 'gm_prob', merge, 'in1')
#workflow.connect(merge,'out', segment,'tissue_prob_maps')
sym_prob = sym_func.clone('sym_prob')
workflow.connect(merge, 'out', sym_prob, 'in_file')
workflow.connect(sym_prob, 'out_link', segment, 'tissue_prob_maps')
workflow.connect(maskflow, ('outputspec.mask_file', pickfirst), segment,
'mask_image')
workflow.connect(inputnode, 'fwhm', smooth, 'fwhm')
#sym_brain = sym_func.clone('sym_brain')
#workflow.connect(realign, 'mean_image', normalize, 'source')
#workflow.connect(maskflow,'fssource.brain',segment,'data')
fssource = maskflow.get_node('fssource')
import nipype.interfaces.freesurfer as fs
convert_brain = pe.Node(interface=fs.ApplyVolTransform(inverse=True),
name='convert')
workflow.connect(fssource, 'brain', convert_brain, 'target_file')
workflow.connect(maskflow, ('outputspec.reg_file', pickfirst),
convert_brain, 'reg_file')
workflow.connect(mean, 'outputspec.mean_image', convert_brain,
'source_file')
convert2nii = pe.Node(fs.MRIConvert(in_type='mgz', out_type='nii'),
name='convert2nii')
workflow.connect(convert_brain, 'transformed_file', convert2nii, 'in_file')
workflow.connect(convert2nii, 'out_file', segment, 'data')
workflow.connect(segment, 'transformation_mat', normalize,
'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_struct,
'parameter_file')
workflow.connect(convert2nii, 'out_file', normalize_struct,
'apply_to_files')
workflow.connect(realign, 'out_file', normalize, 'apply_to_files')
#normalize.inputs.template='/software/spm8/templates/EPI.nii'
workflow.connect(normalize, 'normalized_files', smooth, 'in_files')
#workflow.connect(realign, 'realigned_files', smooth, 'in_files')
artdetect = pe.Node(ra.ArtifactDetect(mask_type='file',
parameter_source='FSL',
use_differences=[True, False],
use_norm=True,
save_plot=True),
name='artdetect')
workflow.connect([(inputnode, artdetect,
[('norm_threshold', 'norm_threshold'),
('zintensity_threshold', 'zintensity_threshold')])])
workflow.connect([(realign, artdetect, [('out_file', 'realigned_files'),
('par_file',
'realignment_parameters')])])
workflow.connect(maskflow, ('outputspec.mask_file', poplist), artdetect,
'mask_file')
"""
Define the outputs of the workflow and connect the nodes to the outputnode
"""
outputnode = pe.Node(niu.IdentityInterface(fields=[
"realignment_parameters", "smoothed_files", "mask_file", "mean_image",
"reg_file", "reg_cost", 'outlier_files', 'outlier_stats',
'outlier_plots', 'norm_components', 'mod_csf', 'unmod_csf', 'mod_wm',
'unmod_wm', 'mod_gm', 'unmod_gm', 'mean', 'normalized_struct',
'struct_in_functional_space', 'normalization_parameters',
'reverse_normalize_parameters'
]),
name="outputspec")
workflow.connect([
(maskflow, outputnode, [("outputspec.reg_file", "reg_file")]),
(maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]),
(maskflow, outputnode, [(("outputspec.mask_file", poplist),
"mask_file")]),
(realign, outputnode, [('par_file', 'realignment_parameters')]),
(smooth, outputnode, [('smoothed_files', 'smoothed_files')]),
(artdetect, outputnode, [('outlier_files', 'outlier_files'),
('statistic_files', 'outlier_stats'),
('plot_files', 'outlier_plots'),
('norm_files', 'norm_components')])
])
workflow.connect(segment, 'modulated_csf_image', outputnode, 'mod_csf')
workflow.connect(segment, 'modulated_wm_image', outputnode, 'mod_wm')
workflow.connect(segment, 'modulated_gm_image', outputnode, 'mod_gm')
workflow.connect(segment, 'normalized_csf_image', outputnode, 'unmod_csf')
workflow.connect(segment, 'normalized_wm_image', outputnode, 'unmod_wm')
workflow.connect(segment, 'normalized_gm_image', outputnode, 'unmod_gm')
workflow.connect(mean, 'outputspec.mean_image', outputnode, 'mean')
workflow.connect(normalize_struct, 'normalized_files', outputnode,
'normalized_struct')
workflow.connect(segment, 'transformation_mat', outputnode,
'normalization_parameters')
workflow.connect(segment, 'inverse_transformation_mat', outputnode,
'reverse_normalize_parameters')
workflow.connect(convert2nii, 'out_file', outputnode,
'struct_in_functional_space')
workflow.inputs.inputspec.fwhm = c.fwhm
workflow.inputs.inputspec.subjects_dir = c.surf_dir
workflow.inputs.inputspec.norm_threshold = c.norm_thresh
workflow.inputs.inputspec.zintensity_threshold = c.z_thresh
workflow.inputs.inputspec.node = c.motion_correct_node
workflow.inputs.inputspec.tr = c.TR
workflow.inputs.inputspec.do_slicetime = c.do_slicetiming
workflow.inputs.inputspec.sliceorder = c.SliceOrder
workflow.inputs.inputspec.csf_prob = c.csf_prob
workflow.inputs.inputspec.gm_prob = c.grey_prob
workflow.inputs.inputspec.wm_prob = c.white_prob
workflow.base_dir = c.working_dir
workflow.config = {'execution': {'crashdump_dir': c.crash_dir}}
datagrabber = get_dataflow(c)
workflow.connect(datagrabber, 'func', inputnode, 'functionals')
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id']),
name='subject_names')
if not c.test_mode:
infosource.iterables = ('subject_id', c.subjects)
else:
infosource.iterables = ('subject_id', c.subjects[:1])
workflow.connect(infosource, 'subject_id', inputnode, 'subject_id')
workflow.connect(infosource, 'subject_id', datagrabber, 'subject_id')
sub = lambda x: [('_subject_id_%s' % x, '')]
sinker = pe.Node(nio.DataSink(), name='sinker')
workflow.connect(infosource, 'subject_id', sinker, 'container')
workflow.connect(infosource, ('subject_id', sub), sinker, 'substitutions')
sinker.inputs.base_directory = c.sink_dir
outputspec = workflow.get_node('outputspec')
workflow.connect(outputspec, 'realignment_parameters', sinker,
'spm_preproc.realignment_parameters')
workflow.connect(outputspec, 'smoothed_files', sinker,
'spm_preproc.smoothed_outputs')
workflow.connect(outputspec, 'outlier_files', sinker,
'spm_preproc.art.@outlier_files')
workflow.connect(outputspec, 'outlier_stats', sinker,
'spm_preproc.art.@outlier_stats')
workflow.connect(outputspec, 'outlier_plots', sinker,
'spm_preproc.art.@outlier_plots')
workflow.connect(outputspec, 'norm_components', sinker,
'spm_preproc.art.@norm')
workflow.connect(outputspec, 'reg_file', sinker,
'spm_preproc.bbreg.@reg_file')
workflow.connect(outputspec, 'reg_cost', sinker,
'spm_preproc.bbreg.@reg_cost')
workflow.connect(outputspec, 'mask_file', sinker,
'spm_preproc.mask.@mask_file')
workflow.connect(outputspec, 'mod_csf', sinker,
'spm_preproc.segment.mod.@csf')
workflow.connect(outputspec, 'mod_wm', sinker,
'spm_preproc.segment.mod.@wm')
workflow.connect(outputspec, 'mod_gm', sinker,
'spm_preproc.segment.mod.@gm')
workflow.connect(outputspec, 'unmod_csf', sinker,
'spm_preproc.segment.unmod.@csf')
workflow.connect(outputspec, 'unmod_wm', sinker,
'spm_preproc.segment.unmod.@wm')
workflow.connect(outputspec, 'unmod_gm', sinker,
'spm_preproc.segment.unmod.@gm')
workflow.connect(outputspec, 'mean', sinker, 'spm_preproc.mean')
workflow.connect(outputspec, 'normalized_struct', sinker,
'spm_preproc.normalized_struct')
workflow.connect(outputspec, 'normalization_parameters', sinker,
'spm_preproc.normalization_parameters.@forward')
workflow.connect(outputspec, 'reverse_normalize_parameters', sinker,
'spm_preproc.normalization_parameters.@reverse')
workflow.connect(outputspec, 'struct_in_functional_space', sinker,
'spm_preproc.struct_in_func_space')
return workflow
def create_spm_preproc(c, name='preproc'):
"""
"""
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
import nipype.algorithms.rapidart as ra
import nipype.interfaces.spm as spm
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
import nipype.interfaces.freesurfer as fs
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=[
'functionals', 'subject_id', 'subjects_dir', 'fwhm', 'norm_threshold',
'zintensity_threshold', 'tr', 'do_slicetime', 'sliceorder',
'parameters', 'node', 'csf_prob', 'wm_prob', 'gm_prob'
]),
name='inputspec')
poplist = lambda x: x.pop()
sym_func = pe.Node(niu.Function(input_names=['in_file'],
output_names=['out_link'],
function=do_symlink),
name='func_symlink')
# REALIGN
realign = pe.Node(niu.Function(
input_names=[
'node', 'in_file', 'tr', 'do_slicetime', 'sliceorder', 'parameters'
],
output_names=['out_file', 'par_file', 'parameter_source'],
function=mod_realign),
name="mod_realign")
workflow.connect(inputnode, 'parameters', realign, 'parameters')
workflow.connect(inputnode, 'functionals', realign, 'in_file')
workflow.connect(inputnode, 'tr', realign, 'tr')
workflow.connect(inputnode, 'do_slicetime', realign, 'do_slicetime')
workflow.connect(inputnode, 'sliceorder', realign, 'sliceorder')
workflow.connect(inputnode, 'node', realign, 'node')
# TAKE MEAN IMAGE
mean = art_mean_workflow()
workflow.connect(realign, 'out_file', mean, 'inputspec.realigned_files')
workflow.connect(realign, 'par_file', mean,
'inputspec.realignment_parameters')
workflow.connect(realign, 'parameter_source', mean,
'inputspec.parameter_source')
# CREATE BRAIN MASK
maskflow = create_getmask_flow()
workflow.connect([(inputnode, maskflow,
[('subject_id', 'inputspec.subject_id'),
('subjects_dir', 'inputspec.subjects_dir')])])
maskflow.inputs.inputspec.contrast_type = 't2'
workflow.connect(mean, 'outputspec.mean_image', maskflow,
'inputspec.source_file')
# SEGMENT
segment = pe.Node(spm.Segment(csf_output_type=[True, True, False],
gm_output_type=[True, True, False],
wm_output_type=[True, True, False]),
name='segment')
mergefunc = lambda in1, in2, in3: [in1, in2, in3]
merge = pe.Node(niu.Function(input_names=['in1', 'in2', 'in3'],
output_names=['out'],
function=mergefunc),
name='merge')
workflow.connect(inputnode, 'csf_prob', merge, 'in3')
workflow.connect(inputnode, 'wm_prob', merge, 'in2')
workflow.connect(inputnode, 'gm_prob', merge, 'in1')
sym_prob = sym_func
workflow.connect(merge, 'out', sym_prob, 'in_file')
workflow.connect(sym_prob, 'out_link', segment, 'tissue_prob_maps')
xform_mask = pe.Node(fs.ApplyVolTransform(fs_target=True),
name='transform_mask')
workflow.connect(maskflow, ('outputspec.reg_file', pickfirst), xform_mask,
'reg_file')
workflow.connect(maskflow, ('outputspec.mask_file', pickfirst), xform_mask,
'source_file')
workflow.connect(xform_mask, "transformed_file", segment, 'mask_image')
fssource = maskflow.get_node('fssource')
convert2nii = pe.Node(fs.MRIConvert(in_type='mgz', out_type='nii'),
name='convert2nii')
workflow.connect(fssource, 'brain', convert2nii, 'in_file')
workflow.connect(convert2nii, 'out_file', segment, 'data')
# NORMALIZE
normalize = pe.MapNode(spm.Normalize(jobtype='write'),
name='normalize',
iterfield=['apply_to_files'])
normalize_struct = normalize.clone('normalize_struct')
normalize_mask = normalize.clone('normalize_mask')
workflow.connect(segment, 'transformation_mat', normalize,
'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_mask,
'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_struct,
'parameter_file')
workflow.connect(convert2nii, 'out_file', normalize_struct,
'apply_to_files')
workflow.connect(xform_mask, "transformed_file", normalize_mask,
'apply_to_files')
xform_image = pe.MapNode(fs.ApplyVolTransform(fs_target=True),
name='xform_image',
iterfield=['source_file'])
workflow.connect(maskflow, ('outputspec.reg_file', pickfirst), xform_image,
'reg_file')
workflow.connect(realign, 'out_file', xform_image, "source_file")
workflow.connect(xform_image, "transformed_file", normalize,
"apply_to_files")
#SMOOTH
smooth = pe.Node(spm.Smooth(), name='smooth')
workflow.connect(inputnode, 'fwhm', smooth, 'fwhm')
workflow.connect(normalize, 'normalized_files', smooth, 'in_files')
# ART
artdetect = pe.Node(ra.ArtifactDetect(mask_type='file',
use_differences=[True, False],
use_norm=True,
save_plot=True),
name='artdetect')
workflow.connect(realign, 'parameter_source', artdetect,
'parameter_source')
workflow.connect([(inputnode, artdetect,
[('norm_threshold', 'norm_threshold'),
('zintensity_threshold', 'zintensity_threshold')])])
workflow.connect([(realign, artdetect, [('out_file', 'realigned_files'),
('par_file',
'realignment_parameters')])])
workflow.connect(maskflow, ('outputspec.mask_file', poplist), artdetect,
'mask_file')
# OUTPUTS
outputnode = pe.Node(niu.IdentityInterface(fields=[
"realignment_parameters", "smoothed_files", "mask_file", "mean_image",
"reg_file", "reg_cost", 'outlier_files', 'outlier_stats',
'outlier_plots', 'norm_components', 'mod_csf', 'unmod_csf', 'mod_wm',
'unmod_wm', 'mod_gm', 'unmod_gm', 'mean', 'normalized_struct',
'normalization_parameters', 'reverse_normalize_parameters'
]),
name="outputspec")
workflow.connect([
(maskflow, outputnode, [("outputspec.reg_file", "reg_file")]),
(maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]),
(realign, outputnode, [('par_file', 'realignment_parameters')]),
(smooth, outputnode, [('smoothed_files', 'smoothed_files')]),
(artdetect, outputnode, [('outlier_files', 'outlier_files'),
('statistic_files', 'outlier_stats'),
('plot_files', 'outlier_plots'),
('norm_files', 'norm_components')])
])
workflow.connect(normalize_mask, "normalized_files", outputnode,
"mask_file")
workflow.connect(segment, 'modulated_csf_image', outputnode, 'mod_csf')
workflow.connect(segment, 'modulated_wm_image', outputnode, 'mod_wm')
workflow.connect(segment, 'modulated_gm_image', outputnode, 'mod_gm')
workflow.connect(segment, 'normalized_csf_image', outputnode, 'unmod_csf')
workflow.connect(segment, 'normalized_wm_image', outputnode, 'unmod_wm')
workflow.connect(segment, 'normalized_gm_image', outputnode, 'unmod_gm')
workflow.connect(mean, 'outputspec.mean_image', outputnode, 'mean')
workflow.connect(normalize_struct, 'normalized_files', outputnode,
'normalized_struct')
workflow.connect(segment, 'transformation_mat', outputnode,
'normalization_parameters')
workflow.connect(segment, 'inverse_transformation_mat', outputnode,
'reverse_normalize_parameters')
# CONNECT TO CONFIG
workflow.inputs.inputspec.fwhm = c.fwhm
workflow.inputs.inputspec.subjects_dir = c.surf_dir
workflow.inputs.inputspec.norm_threshold = c.norm_thresh
workflow.inputs.inputspec.zintensity_threshold = c.z_thresh
workflow.inputs.inputspec.node = c.motion_correct_node
workflow.inputs.inputspec.tr = c.TR
workflow.inputs.inputspec.do_slicetime = c.do_slicetiming
workflow.inputs.inputspec.sliceorder = c.SliceOrder
workflow.inputs.inputspec.csf_prob = c.csf_prob
workflow.inputs.inputspec.gm_prob = c.grey_prob
workflow.inputs.inputspec.wm_prob = c.white_prob
workflow.inputs.inputspec.parameters = {"order": c.order}
workflow.base_dir = c.working_dir
workflow.config = {'execution': {'crashdump_dir': c.crash_dir}}
datagrabber = get_dataflow(c)
workflow.connect(datagrabber, 'func', inputnode, 'functionals')
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id']),
name='subject_names')
if not c.test_mode:
infosource.iterables = ('subject_id', c.subjects)
else:
infosource.iterables = ('subject_id', c.subjects[:1])
workflow.connect(infosource, 'subject_id', inputnode, 'subject_id')
workflow.connect(infosource, 'subject_id', datagrabber, 'subject_id')
sub = lambda x: [('_subject_id_%s' % x, '')]
sinker = pe.Node(nio.DataSink(), name='sinker')
workflow.connect(infosource, 'subject_id', sinker, 'container')
workflow.connect(infosource, ('subject_id', sub), sinker, 'substitutions')
sinker.inputs.base_directory = c.sink_dir
outputspec = workflow.get_node('outputspec')
workflow.connect(outputspec, 'realignment_parameters', sinker,
'spm_preproc.realignment_parameters')
workflow.connect(outputspec, 'smoothed_files', sinker,
'spm_preproc.smoothed_outputs')
workflow.connect(outputspec, 'outlier_files', sinker,
'spm_preproc.art.@outlier_files')
workflow.connect(outputspec, 'outlier_stats', sinker,
'spm_preproc.art.@outlier_stats')
workflow.connect(outputspec, 'outlier_plots', sinker,
'spm_preproc.art.@outlier_plots')
workflow.connect(outputspec, 'norm_components', sinker,
'spm_preproc.art.@norm')
workflow.connect(outputspec, 'reg_file', sinker,
'spm_preproc.bbreg.@reg_file')
workflow.connect(outputspec, 'reg_cost', sinker,
'spm_preproc.bbreg.@reg_cost')
workflow.connect(outputspec, 'mask_file', sinker,
'spm_preproc.mask.@mask_file')
workflow.connect(outputspec, 'mod_csf', sinker,
'spm_preproc.segment.mod.@csf')
workflow.connect(outputspec, 'mod_wm', sinker,
'spm_preproc.segment.mod.@wm')
workflow.connect(outputspec, 'mod_gm', sinker,
'spm_preproc.segment.mod.@gm')
workflow.connect(outputspec, 'unmod_csf', sinker,
'spm_preproc.segment.unmod.@csf')
workflow.connect(outputspec, 'unmod_wm', sinker,
'spm_preproc.segment.unmod.@wm')
workflow.connect(outputspec, 'unmod_gm', sinker,
'spm_preproc.segment.unmod.@gm')
workflow.connect(outputspec, 'mean', sinker, 'spm_preproc.mean')
workflow.connect(outputspec, 'normalized_struct', sinker,
'spm_preproc.normalized_struct')
workflow.connect(outputspec, 'normalization_parameters', sinker,
'spm_preproc.normalization_parameters.@forward')
workflow.connect(outputspec, 'reverse_normalize_parameters', sinker,
'spm_preproc.normalization_parameters.@reverse')
return workflow
def create_spm_preproc(c, name="preproc"):
"""
"""
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
import nipype.algorithms.rapidart as ra
import nipype.interfaces.spm as spm
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
import nipype.interfaces.freesurfer as fs
workflow = pe.Workflow(name=name)
inputnode = pe.Node(
niu.IdentityInterface(
fields=[
"functionals",
"subject_id",
"subjects_dir",
"fwhm",
"norm_threshold",
"zintensity_threshold",
"tr",
"do_slicetime",
"sliceorder",
"parameters",
"node",
"csf_prob",
"wm_prob",
"gm_prob",
]
),
name="inputspec",
)
poplist = lambda x: x.pop()
sym_func = pe.Node(
niu.Function(input_names=["in_file"], output_names=["out_link"], function=do_symlink), name="func_symlink"
)
# REALIGN
realign = pe.Node(
niu.Function(
input_names=["node", "in_file", "tr", "do_slicetime", "sliceorder", "parameters"],
output_names=["out_file", "par_file", "parameter_source"],
function=mod_realign,
),
name="mod_realign",
)
workflow.connect(inputnode, "parameters", realign, "parameters")
workflow.connect(inputnode, "functionals", realign, "in_file")
workflow.connect(inputnode, "tr", realign, "tr")
workflow.connect(inputnode, "do_slicetime", realign, "do_slicetime")
workflow.connect(inputnode, "sliceorder", realign, "sliceorder")
workflow.connect(inputnode, "node", realign, "node")
# TAKE MEAN IMAGE
mean = art_mean_workflow()
workflow.connect(realign, "out_file", mean, "inputspec.realigned_files")
workflow.connect(realign, "par_file", mean, "inputspec.realignment_parameters")
workflow.connect(realign, "parameter_source", mean, "inputspec.parameter_source")
# CREATE BRAIN MASK
maskflow = create_getmask_flow()
workflow.connect(
[(inputnode, maskflow, [("subject_id", "inputspec.subject_id"), ("subjects_dir", "inputspec.subjects_dir")])]
)
maskflow.inputs.inputspec.contrast_type = "t2"
workflow.connect(mean, "outputspec.mean_image", maskflow, "inputspec.source_file")
# SEGMENT
segment = pe.Node(
spm.Segment(
csf_output_type=[True, True, False], gm_output_type=[True, True, False], wm_output_type=[True, True, False]
),
name="segment",
)
mergefunc = lambda in1, in2, in3: [in1, in2, in3]
merge = pe.Node(
niu.Function(input_names=["in1", "in2", "in3"], output_names=["out"], function=mergefunc), name="merge"
)
workflow.connect(inputnode, "csf_prob", merge, "in3")
workflow.connect(inputnode, "wm_prob", merge, "in2")
workflow.connect(inputnode, "gm_prob", merge, "in1")
sym_prob = sym_func
workflow.connect(merge, "out", sym_prob, "in_file")
workflow.connect(sym_prob, "out_link", segment, "tissue_prob_maps")
xform_mask = pe.Node(fs.ApplyVolTransform(fs_target=True), name="transform_mask")
workflow.connect(maskflow, ("outputspec.reg_file", pickfirst), xform_mask, "reg_file")
workflow.connect(maskflow, ("outputspec.mask_file", pickfirst), xform_mask, "source_file")
workflow.connect(xform_mask, "transformed_file", segment, "mask_image")
fssource = maskflow.get_node("fssource")
convert2nii = pe.Node(fs.MRIConvert(in_type="mgz", out_type="nii"), name="convert2nii")
workflow.connect(fssource, "brain", convert2nii, "in_file")
workflow.connect(convert2nii, "out_file", segment, "data")
# NORMALIZE
normalize = pe.MapNode(spm.Normalize(jobtype="write"), name="normalize", iterfield=["apply_to_files"])
normalize_struct = normalize.clone("normalize_struct")
normalize_mask = normalize.clone("normalize_mask")
workflow.connect(segment, "transformation_mat", normalize, "parameter_file")
workflow.connect(segment, "transformation_mat", normalize_mask, "parameter_file")
workflow.connect(segment, "transformation_mat", normalize_struct, "parameter_file")
workflow.connect(convert2nii, "out_file", normalize_struct, "apply_to_files")
workflow.connect(xform_mask, "transformed_file", normalize_mask, "apply_to_files")
xform_image = pe.MapNode(fs.ApplyVolTransform(fs_target=True), name="xform_image", iterfield=["source_file"])
workflow.connect(maskflow, ("outputspec.reg_file", pickfirst), xform_image, "reg_file")
workflow.connect(realign, "out_file", xform_image, "source_file")
workflow.connect(xform_image, "transformed_file", normalize, "apply_to_files")
# SMOOTH
smooth = pe.Node(spm.Smooth(), name="smooth")
workflow.connect(inputnode, "fwhm", smooth, "fwhm")
workflow.connect(normalize, "normalized_files", smooth, "in_files")
# ART
artdetect = pe.Node(
ra.ArtifactDetect(mask_type="file", use_differences=[True, False], use_norm=True, save_plot=True),
name="artdetect",
)
workflow.connect(realign, "parameter_source", artdetect, "parameter_source")
workflow.connect(
[
(
inputnode,
artdetect,
[("norm_threshold", "norm_threshold"), ("zintensity_threshold", "zintensity_threshold")],
)
]
)
workflow.connect([(realign, artdetect, [("out_file", "realigned_files"), ("par_file", "realignment_parameters")])])
workflow.connect(maskflow, ("outputspec.mask_file", poplist), artdetect, "mask_file")
# OUTPUTS
outputnode = pe.Node(
niu.IdentityInterface(
fields=[
"realignment_parameters",
"smoothed_files",
"mask_file",
"mean_image",
"reg_file",
"reg_cost",
"outlier_files",
"outlier_stats",
"outlier_plots",
"norm_components",
"mod_csf",
"unmod_csf",
"mod_wm",
"unmod_wm",
"mod_gm",
"unmod_gm",
"mean",
"normalized_struct",
"normalization_parameters",
"reverse_normalize_parameters",
]
),
name="outputspec",
)
workflow.connect(
[
(maskflow, outputnode, [("outputspec.reg_file", "reg_file")]),
(maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]),
(realign, outputnode, [("par_file", "realignment_parameters")]),
(smooth, outputnode, [("smoothed_files", "smoothed_files")]),
(
artdetect,
outputnode,
[
("outlier_files", "outlier_files"),
("statistic_files", "outlier_stats"),
("plot_files", "outlier_plots"),
("norm_files", "norm_components"),
],
),
]
)
workflow.connect(normalize_mask, "normalized_files", outputnode, "mask_file")
workflow.connect(segment, "modulated_csf_image", outputnode, "mod_csf")
workflow.connect(segment, "modulated_wm_image", outputnode, "mod_wm")
workflow.connect(segment, "modulated_gm_image", outputnode, "mod_gm")
workflow.connect(segment, "normalized_csf_image", outputnode, "unmod_csf")
workflow.connect(segment, "normalized_wm_image", outputnode, "unmod_wm")
workflow.connect(segment, "normalized_gm_image", outputnode, "unmod_gm")
workflow.connect(mean, "outputspec.mean_image", outputnode, "mean")
workflow.connect(normalize_struct, "normalized_files", outputnode, "normalized_struct")
workflow.connect(segment, "transformation_mat", outputnode, "normalization_parameters")
workflow.connect(segment, "inverse_transformation_mat", outputnode, "reverse_normalize_parameters")
# CONNECT TO CONFIG
workflow.inputs.inputspec.fwhm = c.fwhm
workflow.inputs.inputspec.subjects_dir = c.surf_dir
workflow.inputs.inputspec.norm_threshold = c.norm_thresh
workflow.inputs.inputspec.zintensity_threshold = c.z_thresh
workflow.inputs.inputspec.node = c.motion_correct_node
workflow.inputs.inputspec.tr = c.TR
workflow.inputs.inputspec.do_slicetime = c.do_slicetiming
workflow.inputs.inputspec.sliceorder = c.SliceOrder
workflow.inputs.inputspec.csf_prob = c.csf_prob
workflow.inputs.inputspec.gm_prob = c.grey_prob
workflow.inputs.inputspec.wm_prob = c.white_prob
workflow.inputs.inputspec.parameters = {"order": c.order}
workflow.base_dir = c.working_dir
workflow.config = {"execution": {"crashdump_dir": c.crash_dir}}
datagrabber = get_dataflow(c)
workflow.connect(datagrabber, "func", inputnode, "functionals")
infosource = pe.Node(niu.IdentityInterface(fields=["subject_id"]), name="subject_names")
if not c.test_mode:
infosource.iterables = ("subject_id", c.subjects)
else:
infosource.iterables = ("subject_id", c.subjects[:1])
workflow.connect(infosource, "subject_id", inputnode, "subject_id")
workflow.connect(infosource, "subject_id", datagrabber, "subject_id")
sub = lambda x: [("_subject_id_%s" % x, "")]
sinker = pe.Node(nio.DataSink(), name="sinker")
workflow.connect(infosource, "subject_id", sinker, "container")
workflow.connect(infosource, ("subject_id", sub), sinker, "substitutions")
sinker.inputs.base_directory = c.sink_dir
outputspec = workflow.get_node("outputspec")
workflow.connect(outputspec, "realignment_parameters", sinker, "spm_preproc.realignment_parameters")
workflow.connect(outputspec, "smoothed_files", sinker, "spm_preproc.smoothed_outputs")
workflow.connect(outputspec, "outlier_files", sinker, "spm_preproc.art.@outlier_files")
workflow.connect(outputspec, "outlier_stats", sinker, "spm_preproc.art.@outlier_stats")
workflow.connect(outputspec, "outlier_plots", sinker, "spm_preproc.art.@outlier_plots")
workflow.connect(outputspec, "norm_components", sinker, "spm_preproc.art.@norm")
workflow.connect(outputspec, "reg_file", sinker, "spm_preproc.bbreg.@reg_file")
workflow.connect(outputspec, "reg_cost", sinker, "spm_preproc.bbreg.@reg_cost")
workflow.connect(outputspec, "mask_file", sinker, "spm_preproc.mask.@mask_file")
workflow.connect(outputspec, "mod_csf", sinker, "spm_preproc.segment.mod.@csf")
workflow.connect(outputspec, "mod_wm", sinker, "spm_preproc.segment.mod.@wm")
workflow.connect(outputspec, "mod_gm", sinker, "spm_preproc.segment.mod.@gm")
workflow.connect(outputspec, "unmod_csf", sinker, "spm_preproc.segment.unmod.@csf")
workflow.connect(outputspec, "unmod_wm", sinker, "spm_preproc.segment.unmod.@wm")
workflow.connect(outputspec, "unmod_gm", sinker, "spm_preproc.segment.unmod.@gm")
workflow.connect(outputspec, "mean", sinker, "spm_preproc.mean")
workflow.connect(outputspec, "normalized_struct", sinker, "spm_preproc.normalized_struct")
workflow.connect(outputspec, "normalization_parameters", sinker, "spm_preproc.normalization_parameters.@forward")
workflow.connect(
outputspec, "reverse_normalize_parameters", sinker, "spm_preproc.normalization_parameters.@reverse"
)
return workflow
def create_spm_preproc(c, name='preproc'):
"""Create an spm preprocessing workflow with freesurfer registration and
artifact detection.
The workflow realigns and smooths and registers the functional images with
the subject's freesurfer space.
Example
-------
>>> preproc = create_spm_preproc()
>>> preproc.base_dir = '.'
>>> preproc.inputs.inputspec.fwhm = 6
>>> preproc.inputs.inputspec.subject_id = 's1'
>>> preproc.inputs.inputspec.subjects_dir = '.'
>>> preproc.inputs.inputspec.functionals = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.norm_threshold = 1
>>> preproc.inputs.inputspec.zintensity_threshold = 3
Inputs::
inputspec.functionals : functional runs use 4d nifti
inputspec.subject_id : freesurfer subject id
inputspec.subjects_dir : freesurfer subjects dir
inputspec.fwhm : smoothing fwhm
inputspec.norm_threshold : norm threshold for outliers
inputspec.zintensity_threshold : intensity threshold in z-score
Outputs::
outputspec.realignment_parameters : realignment parameter files
outputspec.smoothed_files : smoothed functional files
outputspec.outlier_files : list of outliers
outputspec.outlier_stats : statistics of outliers
outputspec.outlier_plots : images of outliers
outputspec.mask_file : binary mask file in reference image space
outputspec.reg_file : registration file that maps reference image to
freesurfer space
outputspec.reg_cost : cost of registration (useful for detecting misalignment)
"""
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
import nipype.algorithms.rapidart as ra
import nipype.interfaces.spm as spm
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
"""
Initialize the workflow
"""
workflow = pe.Workflow(name=name)
"""
Define the inputs to this workflow
"""
inputnode = pe.Node(niu.IdentityInterface(fields=['functionals',
'subject_id',
'subjects_dir',
'fwhm',
'norm_threshold',
'zintensity_threshold',
'tr',
'do_slicetime',
'sliceorder',
'node',
'csf_prob','wm_prob','gm_prob']),
name='inputspec')
"""
Setup the processing nodes and create the mask generation and coregistration
workflow
"""
poplist = lambda x: x.pop()
#realign = pe.Node(spm.Realign(), name='realign')
sym_func = pe.Node(niu.Function(input_names=['in_file'],output_names=['out_link'],function=do_symlink),name='func_symlink')
realign = pe.Node(niu.Function(input_names=['node','in_file','tr','do_slicetime','sliceorder'],
output_names=['out_file','par_file'],
function=mod_realign),
name="mod_realign")
mean = art_mean_workflow()
workflow.connect(realign,'out_file', mean, 'inputspec.realigned_files')
workflow.connect(realign,'par_file', mean, 'inputspec.realignment_parameters')
mean.inputs.inputspec.parameter_source='FSL' # Modular realign puts it in FSL format for consistency
#workflow.connect(inputnode, 'functionals', realign, 'in_file')
workflow.connect(inputnode,'functionals', sym_func, 'in_file')
workflow.connect(sym_func,'out_link',realign,'in_file')
workflow.connect(inputnode, 'tr',
realign, 'tr')
workflow.connect(inputnode, 'do_slicetime',
realign, 'do_slicetime')
workflow.connect(inputnode, 'sliceorder',
realign, 'sliceorder')
workflow.connect(inputnode, 'node',
realign, 'node')
maskflow = create_getmask_flow()
workflow.connect([(inputnode, maskflow, [('subject_id','inputspec.subject_id'),
('subjects_dir', 'inputspec.subjects_dir')])])
maskflow.inputs.inputspec.contrast_type = 't2'
workflow.connect(mean, 'outputspec.mean_image', maskflow, 'inputspec.source_file')
smooth = pe.Node(spm.Smooth(), name='smooth')
normalize = pe.Node(spm.Normalize(jobtype='write'),name='normalize')
normalize_struct = normalize.clone('normalize_struct')
segment = pe.Node(spm.Segment(csf_output_type=[True,True,False],
gm_output_type=[True,True,False],
wm_output_type=[True,True,False]),name='segment')
mergefunc = lambda in1,in2,in3:[in1,in2,in3]
# merge = pe.Node(niu.Merge(),name='merge')
merge = pe.Node(niu.Function(input_names=['in1','in2','in3'],output_names=['out'],function=mergefunc),name='merge')
workflow.connect(inputnode,'csf_prob',merge,'in3')
workflow.connect(inputnode,'wm_prob',merge,'in2')
workflow.connect(inputnode,'gm_prob',merge,'in1')
#workflow.connect(merge,'out', segment,'tissue_prob_maps')
sym_prob = sym_func.clone('sym_prob')
workflow.connect(merge,'out',sym_prob,'in_file')
workflow.connect(sym_prob,'out_link',segment,'tissue_prob_maps')
workflow.connect(maskflow,('outputspec.mask_file',pickfirst),segment,'mask_image')
workflow.connect(inputnode, 'fwhm', smooth, 'fwhm')
#sym_brain = sym_func.clone('sym_brain')
#workflow.connect(realign, 'mean_image', normalize, 'source')
#workflow.connect(maskflow,'fssource.brain',segment,'data')
fssource = maskflow.get_node('fssource')
import nipype.interfaces.freesurfer as fs
convert_brain = pe.Node(interface=fs.ApplyVolTransform(inverse=True),name='convert')
workflow.connect(fssource,'brain',convert_brain,'target_file')
workflow.connect(maskflow,('outputspec.reg_file',pickfirst),convert_brain,'reg_file')
workflow.connect(mean,'outputspec.mean_image',convert_brain,'source_file')
convert2nii = pe.Node(fs.MRIConvert(in_type='mgz',out_type='nii'),name='convert2nii')
workflow.connect(convert_brain,'transformed_file',convert2nii,'in_file')
workflow.connect(convert2nii,'out_file',segment,'data')
workflow.connect(segment, 'transformation_mat', normalize, 'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_struct, 'parameter_file')
workflow.connect(convert2nii,'out_file',normalize_struct, 'apply_to_files')
workflow.connect(realign,'out_file',normalize, 'apply_to_files')
#normalize.inputs.template='/software/spm8/templates/EPI.nii'
workflow.connect(normalize,'normalized_files',smooth,'in_files')
#workflow.connect(realign, 'realigned_files', smooth, 'in_files')
artdetect = pe.Node(ra.ArtifactDetect(mask_type='file',
parameter_source='FSL',
use_differences=[True,False],
use_norm=True,
save_plot=True),
name='artdetect')
workflow.connect([(inputnode, artdetect,[('norm_threshold', 'norm_threshold'),
('zintensity_threshold',
'zintensity_threshold')])])
workflow.connect([(realign, artdetect, [('out_file', 'realigned_files'),
('par_file',
'realignment_parameters')])])
workflow.connect(maskflow, ('outputspec.mask_file', poplist), artdetect, 'mask_file')
"""
Define the outputs of the workflow and connect the nodes to the outputnode
"""
outputnode = pe.Node(niu.IdentityInterface(fields=["realignment_parameters",
"smoothed_files",
"mask_file",
"mean_image",
"reg_file",
"reg_cost",
'outlier_files',
'outlier_stats',
'outlier_plots',
'norm_components',
'mod_csf',
'unmod_csf',
'mod_wm',
'unmod_wm',
'mod_gm',
'unmod_gm',
'mean',
'normalized_struct',
'struct_in_functional_space',
'normalization_parameters',
'reverse_normalize_parameters'
]),
name="outputspec")
workflow.connect([
(maskflow, outputnode, [("outputspec.reg_file", "reg_file")]),
(maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]),
(maskflow, outputnode, [(("outputspec.mask_file", poplist), "mask_file")]),
(realign, outputnode, [('par_file', 'realignment_parameters')]),
(smooth, outputnode, [('smoothed_files', 'smoothed_files')]),
(artdetect, outputnode,[('outlier_files', 'outlier_files'),
('statistic_files','outlier_stats'),
('plot_files','outlier_plots'),
('norm_files','norm_components')])
])
workflow.connect(segment,'modulated_csf_image',outputnode,'mod_csf')
workflow.connect(segment,'modulated_wm_image',outputnode,'mod_wm')
workflow.connect(segment,'modulated_gm_image',outputnode,'mod_gm')
workflow.connect(segment,'normalized_csf_image',outputnode,'unmod_csf')
workflow.connect(segment,'normalized_wm_image',outputnode,'unmod_wm')
workflow.connect(segment,'normalized_gm_image',outputnode,'unmod_gm')
workflow.connect(mean,'outputspec.mean_image',outputnode, 'mean')
workflow.connect(normalize_struct, 'normalized_files', outputnode, 'normalized_struct')
workflow.connect(segment,'transformation_mat', outputnode,'normalization_parameters')
workflow.connect(segment,'inverse_transformation_mat',outputnode,'reverse_normalize_parameters')
workflow.connect(convert2nii,'out_file',outputnode,'struct_in_functional_space')
workflow.inputs.inputspec.fwhm = c.fwhm
workflow.inputs.inputspec.subjects_dir = c.surf_dir
workflow.inputs.inputspec.norm_threshold = c.norm_thresh
workflow.inputs.inputspec.zintensity_threshold = c.z_thresh
workflow.inputs.inputspec.node = c.motion_correct_node
workflow.inputs.inputspec.tr = c.TR
workflow.inputs.inputspec.do_slicetime = c.do_slicetiming
workflow.inputs.inputspec.sliceorder = c.SliceOrder
workflow.inputs.inputspec.csf_prob = c.csf_prob
workflow.inputs.inputspec.gm_prob = c.grey_prob
workflow.inputs.inputspec.wm_prob = c.white_prob
workflow.base_dir = c.working_dir
workflow.config = {'execution': {'crashdump_dir': c.crash_dir}}
datagrabber = get_dataflow(c)
workflow.connect(datagrabber,'func',inputnode,'functionals')
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id']),
name='subject_names')
if not c.test_mode:
infosource.iterables = ('subject_id', c.subjects)
else:
infosource.iterables = ('subject_id', c.subjects[:1])
workflow.connect(infosource,'subject_id',inputnode,'subject_id')
workflow.connect(infosource,'subject_id',datagrabber,'subject_id')
sub = lambda x: [('_subject_id_%s'%x,'')]
sinker = pe.Node(nio.DataSink(),name='sinker')
workflow.connect(infosource,'subject_id',sinker,'container')
workflow.connect(infosource,('subject_id',sub),sinker,'substitutions')
sinker.inputs.base_directory = c.sink_dir
outputspec = workflow.get_node('outputspec')
workflow.connect(outputspec,'realignment_parameters',sinker,'spm_preproc.realignment_parameters')
workflow.connect(outputspec,'smoothed_files',sinker,'spm_preproc.smoothed_outputs')
workflow.connect(outputspec,'outlier_files',sinker,'spm_preproc.art.@outlier_files')
workflow.connect(outputspec,'outlier_stats',sinker,'spm_preproc.art.@outlier_stats')
workflow.connect(outputspec,'outlier_plots',sinker,'spm_preproc.art.@outlier_plots')
workflow.connect(outputspec,'norm_components',sinker,'spm_preproc.art.@norm')
workflow.connect(outputspec,'reg_file',sinker,'spm_preproc.bbreg.@reg_file')
workflow.connect(outputspec,'reg_cost',sinker,'spm_preproc.bbreg.@reg_cost')
workflow.connect(outputspec,'mask_file',sinker,'spm_preproc.mask.@mask_file')
workflow.connect(outputspec,'mod_csf',sinker,'spm_preproc.segment.mod.@csf')
workflow.connect(outputspec,'mod_wm',sinker,'spm_preproc.segment.mod.@wm')
workflow.connect(outputspec,'mod_gm',sinker,'spm_preproc.segment.mod.@gm')
workflow.connect(outputspec,'unmod_csf',sinker,'spm_preproc.segment.unmod.@csf')
workflow.connect(outputspec,'unmod_wm',sinker,'spm_preproc.segment.unmod.@wm')
workflow.connect(outputspec,'unmod_gm',sinker,'spm_preproc.segment.unmod.@gm')
workflow.connect(outputspec,'mean',sinker,'spm_preproc.mean')
workflow.connect(outputspec,'normalized_struct', sinker, 'spm_preproc.normalized_struct')
workflow.connect(outputspec,'normalization_parameters',sinker,'spm_preproc.normalization_parameters.@forward')
workflow.connect(outputspec,'reverse_normalize_parameters',sinker,'spm_preproc.normalization_parameters.@reverse')
workflow.connect(outputspec,'struct_in_functional_space',sinker,'spm_preproc.struct_in_func_space')
return workflow
def create_spm_preproc(c, name='preproc'):
"""
"""
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
import nipype.algorithms.rapidart as ra
import nipype.interfaces.spm as spm
import nipype.interfaces.utility as niu
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
import nipype.interfaces.freesurfer as fs
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['functionals',
'subject_id',
'subjects_dir',
'fwhm',
'norm_threshold',
'zintensity_threshold',
'tr',
'do_slicetime',
'sliceorder',
'parameters',
'node',
'csf_prob','wm_prob','gm_prob']),
name='inputspec')
poplist = lambda x: x.pop()
sym_func = pe.Node(niu.Function(input_names=['in_file'],output_names=['out_link'],function=do_symlink),name='func_symlink')
# REALIGN
realign = pe.Node(niu.Function(input_names=['node','in_file','tr','do_slicetime','sliceorder','parameters'],
output_names=['out_file','par_file','parameter_source'],
function=mod_realign),
name="mod_realign")
workflow.connect(inputnode,'parameters',realign,'parameters')
workflow.connect(inputnode,'functionals', realign, 'in_file')
workflow.connect(inputnode, 'tr', realign, 'tr')
workflow.connect(inputnode, 'do_slicetime', realign, 'do_slicetime')
workflow.connect(inputnode, 'sliceorder', realign, 'sliceorder')
workflow.connect(inputnode, 'node', realign, 'node')
# TAKE MEAN IMAGE
mean = art_mean_workflow()
workflow.connect(realign,'out_file', mean, 'inputspec.realigned_files')
workflow.connect(realign,'par_file', mean, 'inputspec.realignment_parameters')
workflow.connect(realign,'parameter_source', mean, 'inputspec.parameter_source')
# CREATE BRAIN MASK
maskflow = create_getmask_flow()
workflow.connect([(inputnode, maskflow, [('subject_id','inputspec.subject_id'),
('subjects_dir', 'inputspec.subjects_dir')])])
maskflow.inputs.inputspec.contrast_type = 't2'
workflow.connect(mean, 'outputspec.mean_image', maskflow, 'inputspec.source_file')
# SEGMENT
segment = pe.Node(spm.Segment(csf_output_type=[True,True,False],
gm_output_type=[True,True,False],
wm_output_type=[True,True,False]),name='segment')
mergefunc = lambda in1,in2,in3:[in1,in2,in3]
merge = pe.Node(niu.Function(input_names=['in1','in2','in3'],output_names=['out'],function=mergefunc),name='merge')
workflow.connect(inputnode,'csf_prob',merge,'in3')
workflow.connect(inputnode,'wm_prob',merge,'in2')
workflow.connect(inputnode,'gm_prob',merge,'in1')
sym_prob = sym_func
workflow.connect(merge,'out',sym_prob,'in_file')
workflow.connect(sym_prob,'out_link',segment,'tissue_prob_maps')
xform_mask = pe.Node(fs.ApplyVolTransform(fs_target=True),name='transform_mask')
workflow.connect(maskflow,('outputspec.reg_file',pickfirst),xform_mask,'reg_file')
workflow.connect(maskflow,('outputspec.mask_file',pickfirst),xform_mask,'source_file')
workflow.connect(xform_mask,"transformed_file",segment,'mask_image')
fssource = maskflow.get_node('fssource')
convert2nii = pe.Node(fs.MRIConvert(in_type='mgz',out_type='nii'),name='convert2nii')
workflow.connect(fssource,'brain',convert2nii,'in_file')
workflow.connect(convert2nii,'out_file',segment,'data')
# NORMALIZE
normalize = pe.MapNode(spm.Normalize(jobtype='write'),name='normalize',iterfield=['apply_to_files'])
normalize_struct = normalize.clone('normalize_struct')
normalize_mask = normalize.clone('normalize_mask')
workflow.connect(segment, 'transformation_mat', normalize, 'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_mask, 'parameter_file')
workflow.connect(segment, 'transformation_mat', normalize_struct, 'parameter_file')
workflow.connect(convert2nii,'out_file',normalize_struct, 'apply_to_files')
workflow.connect(xform_mask,"transformed_file",normalize_mask,'apply_to_files')
xform_image = pe.MapNode(fs.ApplyVolTransform(fs_target=True),name='xform_image',iterfield=['source_file'])
workflow.connect(maskflow,('outputspec.reg_file',pickfirst),xform_image,'reg_file')
workflow.connect(realign,'out_file',xform_image,"source_file")
workflow.connect(xform_image,"transformed_file",normalize,"apply_to_files")
#SMOOTH
smooth = pe.Node(spm.Smooth(), name='smooth')
workflow.connect(inputnode, 'fwhm', smooth, 'fwhm')
workflow.connect(normalize,'normalized_files',smooth,'in_files')
# ART
artdetect = pe.Node(ra.ArtifactDetect(mask_type='file',
use_differences=[True,False],
use_norm=True,
save_plot=True),
name='artdetect')
workflow.connect(realign,'parameter_source',artdetect,'parameter_source')
workflow.connect([(inputnode, artdetect,[('norm_threshold', 'norm_threshold'),
('zintensity_threshold',
'zintensity_threshold')])])
workflow.connect([(realign, artdetect, [('out_file', 'realigned_files'),
('par_file',
'realignment_parameters')])])
workflow.connect(maskflow, ('outputspec.mask_file', poplist), artdetect, 'mask_file')
# OUTPUTS
outputnode = pe.Node(niu.IdentityInterface(fields=["realignment_parameters",
"smoothed_files",
"mask_file",
"mean_image",
"reg_file",
"reg_cost",
'outlier_files',
'outlier_stats',
'outlier_plots',
'norm_components',
'mod_csf',
'unmod_csf',
'mod_wm',
'unmod_wm',
'mod_gm',
'unmod_gm',
'mean',
'normalized_struct',
'normalization_parameters',
'reverse_normalize_parameters'
]),
name="outputspec")
workflow.connect([
(maskflow, outputnode, [("outputspec.reg_file", "reg_file")]),
(maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]),
(realign, outputnode, [('par_file', 'realignment_parameters')]),
(smooth, outputnode, [('smoothed_files', 'smoothed_files')]),
(artdetect, outputnode,[('outlier_files', 'outlier_files'),
('statistic_files','outlier_stats'),
('plot_files','outlier_plots'),
('norm_files','norm_components')])
])
workflow.connect(normalize_mask,"normalized_files",outputnode,"mask_file")
workflow.connect(segment,'modulated_csf_image',outputnode,'mod_csf')
workflow.connect(segment,'modulated_wm_image',outputnode,'mod_wm')
workflow.connect(segment,'modulated_gm_image',outputnode,'mod_gm')
workflow.connect(segment,'normalized_csf_image',outputnode,'unmod_csf')
workflow.connect(segment,'normalized_wm_image',outputnode,'unmod_wm')
workflow.connect(segment,'normalized_gm_image',outputnode,'unmod_gm')
workflow.connect(mean,'outputspec.mean_image',outputnode, 'mean')
workflow.connect(normalize_struct, 'normalized_files', outputnode, 'normalized_struct')
workflow.connect(segment,'transformation_mat', outputnode,'normalization_parameters')
workflow.connect(segment,'inverse_transformation_mat',outputnode,'reverse_normalize_parameters')
# CONNECT TO CONFIG
workflow.inputs.inputspec.fwhm = c.fwhm
workflow.inputs.inputspec.subjects_dir = c.surf_dir
workflow.inputs.inputspec.norm_threshold = c.norm_thresh
workflow.inputs.inputspec.zintensity_threshold = c.z_thresh
workflow.inputs.inputspec.node = c.motion_correct_node
workflow.inputs.inputspec.tr = c.TR
workflow.inputs.inputspec.do_slicetime = c.do_slicetiming
workflow.inputs.inputspec.sliceorder = c.SliceOrder
workflow.inputs.inputspec.csf_prob = c.csf_prob
workflow.inputs.inputspec.gm_prob = c.grey_prob
workflow.inputs.inputspec.wm_prob = c.white_prob
workflow.inputs.inputspec.parameters = {"order": c.order}
workflow.base_dir = c.working_dir
workflow.config = {'execution': {'crashdump_dir': c.crash_dir}}
datagrabber = get_dataflow(c)
workflow.connect(datagrabber,'func',inputnode,'functionals')
infosource = pe.Node(niu.IdentityInterface(fields=['subject_id']),
name='subject_names')
if not c.test_mode:
infosource.iterables = ('subject_id', c.subjects)
else:
infosource.iterables = ('subject_id', c.subjects[:1])
workflow.connect(infosource,'subject_id',inputnode,'subject_id')
workflow.connect(infosource,'subject_id',datagrabber,'subject_id')
sub = lambda x: [('_subject_id_%s'%x,'')]
sinker = pe.Node(nio.DataSink(),name='sinker')
workflow.connect(infosource,'subject_id',sinker,'container')
workflow.connect(infosource,('subject_id',sub),sinker,'substitutions')
sinker.inputs.base_directory = c.sink_dir
outputspec = workflow.get_node('outputspec')
workflow.connect(outputspec,'realignment_parameters',sinker,'spm_preproc.realignment_parameters')
workflow.connect(outputspec,'smoothed_files',sinker,'spm_preproc.smoothed_outputs')
workflow.connect(outputspec,'outlier_files',sinker,'spm_preproc.art.@outlier_files')
workflow.connect(outputspec,'outlier_stats',sinker,'spm_preproc.art.@outlier_stats')
workflow.connect(outputspec,'outlier_plots',sinker,'spm_preproc.art.@outlier_plots')
workflow.connect(outputspec,'norm_components',sinker,'spm_preproc.art.@norm')
workflow.connect(outputspec,'reg_file',sinker,'spm_preproc.bbreg.@reg_file')
workflow.connect(outputspec,'reg_cost',sinker,'spm_preproc.bbreg.@reg_cost')
workflow.connect(outputspec,'mask_file',sinker,'spm_preproc.mask.@mask_file')
workflow.connect(outputspec,'mod_csf',sinker,'spm_preproc.segment.mod.@csf')
workflow.connect(outputspec,'mod_wm',sinker,'spm_preproc.segment.mod.@wm')
workflow.connect(outputspec,'mod_gm',sinker,'spm_preproc.segment.mod.@gm')
workflow.connect(outputspec,'unmod_csf',sinker,'spm_preproc.segment.unmod.@csf')
workflow.connect(outputspec,'unmod_wm',sinker,'spm_preproc.segment.unmod.@wm')
workflow.connect(outputspec,'unmod_gm',sinker,'spm_preproc.segment.unmod.@gm')
workflow.connect(outputspec,'mean',sinker,'spm_preproc.mean')
workflow.connect(outputspec,'normalized_struct', sinker, 'spm_preproc.normalized_struct')
workflow.connect(outputspec,'normalization_parameters',sinker,'spm_preproc.normalization_parameters.@forward')
workflow.connect(outputspec,'reverse_normalize_parameters',sinker,'spm_preproc.normalization_parameters.@reverse')
return workflow
def simple_preproc(c):
from .fmri_preprocessing import extract_meta
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
from ...scripts.modular_nodes import mod_realign
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
from ...scripts.utils import art_mean_workflow
from nipype.algorithms.misc import TSNR
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
wf = pe.Workflow(name='simple_preproc')
datagrabber = c.datagrabber.create_dataflow()
infosource = datagrabber.get_node('subject_id_iterable')
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
motion_correct = pe.Node(util.Function(input_names=['node','in_file','tr',
'do_slicetime','sliceorder',"parameters"],
output_names=['out_file','par_file','parameter_source'],
function=mod_realign),
name="mod_realign")
meanfunc = art_mean_workflow()
art = meanfunc.get_node('strict_artifact_detect')
getmask = create_getmask_flow()
tsnr = pe.MapNode(TSNR(regress_poly=2), #SG: advanced parameter
name='tsnr',
iterfield=['in_file'])
if c.use_metadata:
get_meta = pe.Node(util.Function(input_names=['func'],output_names=['so','tr'],function=extract_meta),name="get_metadata")
wf.connect(datagrabber,'datagrabber.epi',get_meta, 'func')
wf.connect(get_meta,'so',motion_correct,"sliceorder")
wf.connect(get_meta,'tr',motion_correct,"tr")
else:
motion_correct.inputs.sliceorder = c.SliceOrder
motion_correct.inputs.tr = c.TR
# inputs
motion_correct.inputs.do_slicetime = c.do_slicetiming
motion_correct.inputs.node = c.motion_correct_node
motion_correct.inputs.parameters = {"loops":c.loops,
"speedup":c.speedup,
"order": c.order}
wf.connect(datagrabber,'datagrabber.epi',img2float,'in_file')
wf.connect(img2float,'out_file', motion_correct,'in_file')
wf.connect(motion_correct,'out_file',meanfunc,'inputspec.realigned_files')
wf.connect(motion_correct,'parameter_source',meanfunc,'inputspec.parameter_source')
wf.connect(motion_correct,'par_file',meanfunc,'inputspec.realignment_parameters')
wf.connect(motion_correct,'out_file',tsnr,'in_file')
wf.connect(meanfunc,'outputspec.mean_image',getmask,'inputspec.source_file')
wf.connect(infosource,'subject_id',getmask,'inputspec.subject_id')
getmask.inputs.inputspec.subjects_dir = c.surf_dir
getmask.inputs.inputspec.contrast_type = 't2'
sink = pe.Node(nio.DataSink(),name='sinker')
sink.inputs.base_directory = c.sink_dir
wf.connect(infosource,'subject_id',sink,'container')
wf.connect(infosource,('subject_id', get_substitutions),sink,'substitutions')
wf.connect(motion_correct,'out_file',sink,'simple_preproc.output')
wf.connect(motion_correct,'par_file',sink,'simple_preproc.motion')
wf.connect(meanfunc,'outputspec.mean_image',sink,'simple_preproc.mean')
wf.connect(getmask,'outputspec.mask_file',sink,'simple_preproc.mask')
wf.connect(getmask,'outputspec.reg_file',sink,'simple_preproc.bbreg.@reg')
wf.connect(getmask,'outputspec.reg_cost',sink,'simple_preproc.bbreg.@regcost')
wf.connect(tsnr,'tsnr_file',sink,'simple_preproc.tsnr.@tsnr')
wf.connect(tsnr,'detrended_file',sink,'simple_preproc.tsnr.@detrended')
wf.connect(tsnr,'stddev_file',sink,'simple_preproc.tsnr.@stddev')
wf.connect(tsnr,'mean_file',sink,'simple_preproc.tsnr.@mean')
wf.connect(art,'intensity_files',sink,'simple_preproc.art.@intensity')
wf.connect(art,'norm_files',sink,'simple_preproc.art.@norm')
wf.connect(art,'outlier_files',sink,'simple_preproc.art.@outlier')
wf.connect(art,'statistic_files',sink,'simple_preproc.art.@stats')
return wf
def simple_preproc(c):
from .fmri_preprocessing import extract_meta
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
from ...scripts.modular_nodes import mod_realign
from nipype.workflows.smri.freesurfer.utils import create_getmask_flow
from ...scripts.utils import art_mean_workflow
from nipype.algorithms.misc import TSNR
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
wf = pe.Workflow(name='simple_preproc')
datagrabber = c.datagrabber.create_dataflow()
infosource = datagrabber.get_node('subject_id_iterable')
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
motion_correct = pe.Node(util.Function(
input_names=[
'node', 'in_file', 'tr', 'do_slicetime', 'sliceorder', "parameters"
],
output_names=['out_file', 'par_file', 'parameter_source'],
function=mod_realign),
name="mod_realign")
meanfunc = art_mean_workflow()
art = meanfunc.get_node('strict_artifact_detect')
getmask = create_getmask_flow()
tsnr = pe.MapNode(
TSNR(regress_poly=2), #SG: advanced parameter
name='tsnr',
iterfield=['in_file'])
if c.use_metadata:
get_meta = pe.Node(util.Function(input_names=['func'],
output_names=['so', 'tr'],
function=extract_meta),
name="get_metadata")
wf.connect(datagrabber, 'datagrabber.epi', get_meta, 'func')
wf.connect(get_meta, 'so', motion_correct, "sliceorder")
wf.connect(get_meta, 'tr', motion_correct, "tr")
else:
motion_correct.inputs.sliceorder = c.SliceOrder
motion_correct.inputs.tr = c.TR
# inputs
motion_correct.inputs.do_slicetime = c.do_slicetiming
motion_correct.inputs.node = c.motion_correct_node
motion_correct.inputs.parameters = {
"loops": c.loops,
"speedup": c.speedup,
"order": c.order
}
wf.connect(datagrabber, 'datagrabber.epi', img2float, 'in_file')
wf.connect(img2float, 'out_file', motion_correct, 'in_file')
wf.connect(motion_correct, 'out_file', meanfunc,
'inputspec.realigned_files')
wf.connect(motion_correct, 'parameter_source', meanfunc,
'inputspec.parameter_source')
wf.connect(motion_correct, 'par_file', meanfunc,
'inputspec.realignment_parameters')
wf.connect(motion_correct, 'out_file', tsnr, 'in_file')
wf.connect(meanfunc, 'outputspec.mean_image', getmask,
'inputspec.source_file')
wf.connect(infosource, 'subject_id', getmask, 'inputspec.subject_id')
getmask.inputs.inputspec.subjects_dir = c.surf_dir
getmask.inputs.inputspec.contrast_type = 't2'
sink = pe.Node(nio.DataSink(), name='sinker')
sink.inputs.base_directory = c.sink_dir
wf.connect(infosource, 'subject_id', sink, 'container')
wf.connect(infosource, ('subject_id', get_substitutions), sink,
'substitutions')
wf.connect(motion_correct, 'out_file', sink, 'simple_preproc.output')
wf.connect(motion_correct, 'par_file', sink, 'simple_preproc.motion')
wf.connect(meanfunc, 'outputspec.mean_image', sink, 'simple_preproc.mean')
wf.connect(getmask, 'outputspec.mask_file', sink, 'simple_preproc.mask')
wf.connect(getmask, 'outputspec.reg_file', sink,
'simple_preproc.bbreg.@reg')
wf.connect(getmask, 'outputspec.reg_cost', sink,
'simple_preproc.bbreg.@regcost')
wf.connect(tsnr, 'tsnr_file', sink, 'simple_preproc.tsnr.@tsnr')
wf.connect(tsnr, 'detrended_file', sink, 'simple_preproc.tsnr.@detrended')
wf.connect(tsnr, 'stddev_file', sink, 'simple_preproc.tsnr.@stddev')
wf.connect(tsnr, 'mean_file', sink, 'simple_preproc.tsnr.@mean')
wf.connect(art, 'intensity_files', sink, 'simple_preproc.art.@intensity')
wf.connect(art, 'norm_files', sink, 'simple_preproc.art.@norm')
wf.connect(art, 'outlier_files', sink, 'simple_preproc.art.@outlier')
wf.connect(art, 'statistic_files', sink, 'simple_preproc.art.@stats')
return wf
