def create_moco_pipeline(name='motion_correction'):
# initiate workflow
moco = Workflow(name='motion_correction')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# inputnode
inputnode = Node(util.IdentityInterface(fields=['epi']), name='inputnode')
# outputnode
outputnode = Node(util.IdentityInterface(fields=[
'epi_moco', 'par_moco', 'mat_moco', 'rms_moco', 'epi_mean', 'rotplot',
'transplot', 'dispplots', 'tsnr_file'
]),
name='outputnode')
# mcflirt motion correction to 1st volume
mcflirt = Node(fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
ref_vol=1,
out_file='rest_realigned.nii.gz'),
name='mcflirt')
# plot motion parameters
rotplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='rotations',
out_file='rotation_plot.png'),
name='rotplotter')
transplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='translations',
out_file='translation_plot.png'),
name='transplotter')
dispplotter = MapNode(interface=fsl.PlotMotionParams(
in_source='fsl',
plot_type='displacement',
),
name='dispplotter',
iterfield=['in_file'])
dispplotter.iterables = ('plot_type', ['displacement'])
# calculate tmean
tmean = Node(fsl.maths.MeanImage(dimension='T',
out_file='rest_realigned_mean.nii.gz'),
name='tmean')
# calculate tsnr
tsnr = Node(confounds.TSNR(), name='tsnr')
# create connections
moco.connect([(inputnode, mcflirt, [('epi', 'in_file')]),
(mcflirt, tmean, [('out_file', 'in_file')]),
(mcflirt, rotplotter, [('par_file', 'in_file')]),
(mcflirt, transplotter, [('par_file', 'in_file')]),
(mcflirt, dispplotter, [('rms_files', 'in_file')]),
(tmean, outputnode, [('out_file', 'epi_mean')]),
(mcflirt, outputnode, [('out_file', 'epi_moco'),
('par_file', 'par_moco'),
('mat_file', 'mat_moco'),
('rms_files', 'rms_moco')]),
(rotplotter, outputnode, [('out_file', 'rotplot')]),
(transplotter, outputnode, [('out_file', 'transplot')]),
(dispplotter, outputnode, [('out_file', 'dispplots')]),
(mcflirt, tsnr, [('out_file', 'in_file')]),
(tsnr, outputnode, [('tsnr_file', 'tsnr_file')])])
return moco
def MCORRECTOR():
#--- 1) Import modules
import nipype.pipeline.engine as pe
import os
os.system('clear')
from glob import glob
import nipype.interfaces.fsl as fsl
import nipype.interfaces.utility as util
#--- 2) Record intial working directory
INITDIR=os.getcwd();
#--- 3) Prompt user for directory containing DICOM FILES
NIFTIFILE=raw_input('Please drag in the nifti\n file you wish to motion correct\n(ensure there is no blank space at the end)\n')
os.system('clear')
print '---\n'
NIFTIFILE=NIFTIFILE.strip('\'"')
NIFTIDIR=os.path.split(NIFTIFILE)[0]
#--- 3) Move to directory
os.chdir(NIFTIDIR)
#--- 4) Set up motion correction node
motion_correct = pe.Node(interface=fsl.MCFLIRT(save_mats=True,save_plots=True,interpolation='spline'),name='MCORRECTED')
motion_correct.inputs.in_file=NIFTIFILE
#--- 5) Set up plotting node
plot_motion = pe.Node(interface=fsl.PlotMotionParams(in_source='fsl'),name='PLOTTED')
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
#--- 5) Utility output node
outputnode = pe.Node(interface=util.IdentityInterface(fields=['mcorrected_files']),name='outputnode')
#--- 6) Set up workflow
workflow = pe.Workflow(name='MCORRECTOR')
workflow.base_dir = NIFTIDIR
#--- 7) Connect nodes.
workflow.connect(motion_correct, 'par_file', plot_motion, 'in_file')
workflow.connect(motion_correct,'out_file', outputnode,'mcorrected_files')
workflow.write_graph(graph2use='exec')
#--- 8) Run workflow
result=workflow.run()
print "Node completed. Returning to intital directory\n"
os.chdir(INITDIR)
def create_workflow(func_runs,
subject_id,
subjects_dir,
fwhm,
slice_times,
highpass_frequency,
lowpass_frequency,
TR,
sink_directory,
use_fsl_bp,
num_components,
whichvol,
name='wmaze'):
wf = pe.Workflow(name=name)
datasource = pe.Node(nio.DataGrabber(infields=['subject_id', 'run'],
outfields=['func']),
name='datasource')
datasource.inputs.subject_id = subject_id
datasource.inputs.run = func_runs
datasource.inputs.template = '/home/data/madlab/data/mri/wmaze/%s/bold/bold_%03d/bold.nii.gz'
datasource.inputs.sort_filelist = True
# Rename files in case they are named identically
name_unique = pe.MapNode(util.Rename(format_string='wmaze_%(run)02d'),
iterfield = ['in_file', 'run'],
name='rename')
name_unique.inputs.keep_ext = True
name_unique.inputs.run = func_runs
wf.connect(datasource, 'func', name_unique, 'in_file')
# Define the outputs for the preprocessing workflow
output_fields = ['reference',
'motion_parameters',
'motion_parameters_plusDerivs',
'motionandoutlier_noise_file',
'noise_components',
'realigned_files',
'motion_plots',
'mask_file',
'smoothed_files',
'bandpassed_files',
'reg_file',
'reg_cost',
'reg_fsl_file',
'artnorm_files',
'artoutlier_files',
'artdisplacement_files',
'tsnr_file']
outputnode = pe.Node(util.IdentityInterface(fields=output_fields),
name='outputspec')
# Convert functional images to float representation
img2float = pe.MapNode(fsl.ImageMaths(out_data_type='float',
op_string = '',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
wf.connect(name_unique, 'out_file', img2float, 'in_file')
# Run AFNI's despike. This is always run, however, whether this is fed to
# realign depends on the input configuration
despiker = pe.MapNode(afni.Despike(outputtype='NIFTI_GZ'),
iterfield=['in_file'],
name='despike')
num_threads = 4
despiker.inputs.environ = {'OMP_NUM_THREADS': '%d' % num_threads}
despiker.plugin_args = {'bsub_args': '-n %d' % num_threads}
despiker.plugin_args = {'bsub_args': '-R "span[hosts=1]"'}
wf.connect(img2float, 'out_file', despiker, 'in_file')
# Extract the first volume of the first run as the reference
extractref = pe.Node(fsl.ExtractROI(t_size=1),
iterfield=['in_file'],
name = "extractref")
wf.connect(despiker, ('out_file', pickfirst), extractref, 'in_file')
wf.connect(despiker, ('out_file', pickvol, 0, whichvol), extractref, 't_min')
wf.connect(extractref, 'roi_file', outputnode, 'reference')
if slice_times is not None:
# Simultaneous motion and slice timing correction with Nipy algorithm
motion_correct = pe.Node(nipy.SpaceTimeRealigner(), name='motion_correct')
motion_correct.inputs.tr = TR
motion_correct.inputs.slice_times = slice_times
motion_correct.inputs.slice_info = 2
motion_correct.plugin_args = {'bsub_args': '-n %s' %os.environ['MKL_NUM_THREADS']}
motion_correct.plugin_args = {'bsub_args': '-R "span[hosts=1]"'}
wf.connect(despiker, 'out_file', motion_correct, 'in_file')
wf.connect(motion_correct, 'par_file', outputnode, 'motion_parameters')
wf.connect(motion_correct, 'out_file', outputnode, 'realigned_files')
else:
# Motion correct functional runs to the reference (1st volume of 1st run)
motion_correct = pe.MapNode(fsl.MCFLIRT(save_mats = True,
save_plots = True,
interpolation = 'sinc'),
name = 'motion_correct',
iterfield = ['in_file'])
wf.connect(despiker, 'out_file', motion_correct, 'in_file')
wf.connect(extractref, 'roi_file', motion_correct, 'ref_file')
wf.connect(motion_correct, 'par_file', outputnode, 'motion_parameters')
wf.connect(motion_correct, 'out_file', outputnode, 'realigned_files')
# Compute TSNR on realigned data regressing polynomials upto order 2
tsnr = pe.MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
wf.connect(motion_correct, 'out_file', tsnr, 'in_file')
wf.connect(tsnr, 'tsnr_file', outputnode, 'tsnr_file')
# Plot the estimated motion parameters
plot_motion = pe.MapNode(fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
wf.connect(motion_correct, 'par_file', plot_motion, 'in_file')
wf.connect(plot_motion, 'out_file', outputnode, 'motion_plots')
# Register a source file to fs space and create a brain mask in source space
fssource = pe.Node(nio.FreeSurferSource(),
name ='fssource')
fssource.inputs.subject_id = subject_id
fssource.inputs.subjects_dir = subjects_dir
# Extract aparc+aseg brain mask and binarize
fs_threshold = pe.Node(fs.Binarize(min=0.5, out_type='nii'),
name ='fs_threshold')
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), fs_threshold, 'in_file')
# Calculate the transformation matrix from EPI space to FreeSurfer space
# using the BBRegister command
fs_register = pe.MapNode(fs.BBRegister(init='fsl'),
iterfield=['source_file'],
name ='fs_register')
fs_register.inputs.contrast_type = 't2'
fs_register.inputs.out_fsl_file = True
fs_register.inputs.subject_id = subject_id
fs_register.inputs.subjects_dir = subjects_dir
wf.connect(extractref, 'roi_file', fs_register, 'source_file')
wf.connect(fs_register, 'out_reg_file', outputnode, 'reg_file')
wf.connect(fs_register, 'min_cost_file', outputnode, 'reg_cost')
wf.connect(fs_register, 'out_fsl_file', outputnode, 'reg_fsl_file')
# Extract wm+csf, brain masks by eroding freesurfer lables
wmcsf = pe.MapNode(fs.Binarize(),
iterfield=['match', 'binary_file', 'erode'], name='wmcsfmask')
#wmcsf.inputs.wm_ven_csf = True
wmcsf.inputs.match = [[2, 41], [4, 5, 14, 15, 24, 31, 43, 44, 63]]
wmcsf.inputs.binary_file = ['wm.nii.gz', 'csf.nii.gz']
wmcsf.inputs.erode = [2, 2] #int(np.ceil(slice_thickness))
wf.connect(fssource, ('aparc_aseg', get_aparc_aseg), wmcsf, 'in_file')
# Now transform the wm and csf masks to 1st volume of 1st run
wmcsftransform = pe.MapNode(fs.ApplyVolTransform(inverse=True,
interp='nearest'),
iterfield=['target_file'],
name='wmcsftransform')
wmcsftransform.inputs.subjects_dir = subjects_dir
wf.connect(extractref, 'roi_file', wmcsftransform, 'source_file')
wf.connect(fs_register, ('out_reg_file', pickfirst), wmcsftransform, 'reg_file')
wf.connect(wmcsf, 'binary_file', wmcsftransform, 'target_file')
# Transform the binarized aparc+aseg file to the 1st volume of 1st run space
fs_voltransform = pe.MapNode(fs.ApplyVolTransform(inverse=True),
iterfield = ['source_file', 'reg_file'],
name='fs_transform')
fs_voltransform.inputs.subjects_dir = subjects_dir
wf.connect(extractref, 'roi_file', fs_voltransform, 'source_file')
wf.connect(fs_register, 'out_reg_file', fs_voltransform, 'reg_file')
wf.connect(fs_threshold, 'binary_file', fs_voltransform, 'target_file')
# Dilate the binarized mask by 1 voxel that is now in the EPI space
fs_threshold2 = pe.MapNode(fs.Binarize(min=0.5, out_type='nii'),
iterfield=['in_file'],
name='fs_threshold2')
fs_threshold2.inputs.dilate = 1
wf.connect(fs_voltransform, 'transformed_file', fs_threshold2, 'in_file')
wf.connect(fs_threshold2, 'binary_file', outputnode, 'mask_file')
# Use RapidART to detect motion/intensity outliers
art = pe.MapNode(ra.ArtifactDetect(use_differences = [True, False],
use_norm = True,
zintensity_threshold = 3,
norm_threshold = 1,
bound_by_brainmask=True,
mask_type = "file"),
iterfield=["realignment_parameters","realigned_files"],
name="art")
if slice_times is not None:
art.inputs.parameter_source = "NiPy"
else:
art.inputs.parameter_source = "FSL"
wf.connect(motion_correct, 'par_file', art, 'realignment_parameters')
wf.connect(motion_correct, 'out_file', art, 'realigned_files')
wf.connect(fs_threshold2, ('binary_file', pickfirst), art, 'mask_file')
wf.connect(art, 'norm_files', outputnode, 'artnorm_files')
wf.connect(art, 'outlier_files', outputnode, 'artoutlier_files')
wf.connect(art, 'displacement_files', outputnode, 'artdisplacement_files')
# Compute motion regressors (save file with 1st and 2nd derivatives)
motreg = pe.Node(util.Function(input_names=['motion_params', 'order',
'derivatives'],
output_names=['out_files'],
function=motion_regressors,
imports=imports),
name='getmotionregress')
wf.connect(motion_correct, 'par_file', motreg, 'motion_params')
wf.connect(motreg, 'out_files', outputnode, 'motion_parameters_plusDerivs')
# Create a filter text file to remove motion (+ derivatives), art confounds,
# and 1st, 2nd, and 3rd order legendre polynomials.
createfilter1 = pe.Node(util.Function(input_names=['motion_params', 'comp_norm',
'outliers', 'detrend_poly'],
output_names=['out_files'],
function=build_filter1,
imports=imports),
name='makemotionbasedfilter')
createfilter1.inputs.detrend_poly = 3
wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
wf.connect(art, 'outlier_files', createfilter1, 'outliers')
wf.connect(createfilter1, 'out_files', outputnode, 'motionandoutlier_noise_file')
# Create a filter to remove noise components based on white matter and CSF
createfilter2 = pe.MapNode(util.Function(input_names=['realigned_file', 'mask_file',
'num_components',
'extra_regressors'],
output_names=['out_files'],
function=extract_noise_components,
imports=imports),
iterfield=['realigned_file', 'extra_regressors'],
name='makecompcorrfilter')
createfilter2.inputs.num_components = num_components
wf.connect(createfilter1, 'out_files', createfilter2, 'extra_regressors')
wf.connect(motion_correct, 'out_file', createfilter2, 'realigned_file')
wf.connect(wmcsftransform, 'transformed_file', createfilter2, 'mask_file')
wf.connect(createfilter2, 'out_files', outputnode, 'noise_components')
# Mask the functional runs with the extracted mask
maskfunc = pe.MapNode(fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file'],
name = 'maskfunc')
wf.connect(motion_correct, 'out_file', maskfunc, 'in_file')
wf.connect(fs_threshold2, ('binary_file', pickfirst), maskfunc, 'in_file2')
# Smooth each run using SUSAn with the brightness threshold set to 75%
# of the median value for each run and a mask constituting the mean functional
smooth_median = pe.MapNode(fsl.ImageStats(op_string='-k %s -p 50'),
iterfield = ['in_file'],
name='smooth_median')
wf.connect(maskfunc, 'out_file', smooth_median, 'in_file')
wf.connect(fs_threshold2, ('binary_file', pickfirst), smooth_median, 'mask_file')
smooth_meanfunc = pe.MapNode(fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='smooth_meanfunc')
wf.connect(maskfunc, 'out_file', smooth_meanfunc, 'in_file')
smooth_merge = pe.Node(util.Merge(2, axis='hstack'),
name='smooth_merge')
wf.connect(smooth_meanfunc, 'out_file', smooth_merge, 'in1')
wf.connect(smooth_median, 'out_stat', smooth_merge, 'in2')
smooth = pe.MapNode(fsl.SUSAN(),
iterfield=['in_file', 'brightness_threshold', 'usans'],
name='smooth')
smooth.inputs.fwhm=fwhm
wf.connect(maskfunc, 'out_file', smooth, 'in_file')
wf.connect(smooth_median, ('out_stat', getbtthresh), smooth, 'brightness_threshold')
wf.connect(smooth_merge, ('out', getusans), smooth, 'usans')
# Mask the smoothed data with the dilated mask
maskfunc2 = pe.MapNode(fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file'],
name='maskfunc2')
wf.connect(smooth, 'smoothed_file', maskfunc2, 'in_file')
wf.connect(fs_threshold2, ('binary_file', pickfirst), maskfunc2, 'in_file2')
wf.connect(maskfunc2, 'out_file', outputnode, 'smoothed_files')
# Band-pass filter the timeseries
if use_fsl_bp == 'True':
determine_bp_sigmas = pe.Node(util.Function(input_names=['tr',
'highpass_freq',
'lowpass_freq'],
output_names = ['out_sigmas'],
function=calc_fslbp_sigmas),
name='determine_bp_sigmas')
determine_bp_sigmas.inputs.tr = float(TR)
determine_bp_sigmas.inputs.highpass_freq = float(highpass_frequency)
determine_bp_sigmas.inputs.lowpass_freq = float(lowpass_frequency)
bandpass = pe.MapNode(fsl.ImageMaths(suffix='_tempfilt'),
iterfield=["in_file"],
name="bandpass")
wf.connect(determine_bp_sigmas, ('out_sigmas', highpass_operand), bandpass, 'op_string')
wf.connect(maskfunc2, 'out_file', bandpass, 'in_file')
wf.connect(bandpass, 'out_file', outputnode, 'bandpassed_files')
else:
bandpass = pe.Node(util.Function(input_names=['files',
'lowpass_freq',
'highpass_freq',
'fs'],
output_names=['out_files'],
function=bandpass_filter,
imports=imports),
name='bandpass')
bandpass.inputs.fs = 1./TR
if highpass_frequency < 0:
bandpass.inputs.highpass_freq = -1
else:
bandpass.inputs.highpass_freq = highpass_frequency
if lowpass_frequency < 0:
bandpass.inputs.lowpass_freq = -1
else:
bandpass.inputs.lowpass_freq = lowpass_frequency
wf.connect(maskfunc2, 'out_file', bandpass, 'files')
wf.connect(bandpass, 'out_files', outputnode, 'bandpassed_files')
# Save the relevant data into an output directory
datasink = pe.Node(nio.DataSink(), name="datasink")
datasink.inputs.base_directory = sink_directory
datasink.inputs.container = subject_id
wf.connect(outputnode, 'reference', datasink, 'ref')
wf.connect(outputnode, 'motion_parameters', datasink, 'motion')
wf.connect(outputnode, 'realigned_files', datasink, 'func.realigned')
wf.connect(outputnode, 'motion_plots', datasink, 'motion.@plots')
wf.connect(outputnode, 'mask_file', datasink, 'ref.@mask')
wf.connect(outputnode, 'smoothed_files', datasink, 'func.smoothed_fullspectrum')
wf.connect(outputnode, 'bandpassed_files', datasink, 'func.smoothed_bandpassed')
wf.connect(outputnode, 'reg_file', datasink, 'bbreg.@reg')
wf.connect(outputnode, 'reg_cost', datasink, 'bbreg.@cost')
wf.connect(outputnode, 'reg_fsl_file', datasink, 'bbreg.@regfsl')
wf.connect(outputnode, 'artnorm_files', datasink, 'art.@norm_files')
wf.connect(outputnode, 'artoutlier_files', datasink, 'art.@outlier_files')
wf.connect(outputnode, 'artdisplacement_files', datasink, 'art.@displacement_files')
wf.connect(outputnode, 'motion_parameters_plusDerivs', datasink, 'noise.@motionplusDerivs')
wf.connect(outputnode, 'motionandoutlier_noise_file', datasink, 'noise.@motionplusoutliers')
wf.connect(outputnode, 'noise_components', datasink, 'compcor')
wf.connect(outputnode, 'tsnr_file', datasink, 'tsnr')
return wf
def FUNCPIPE():
#--- 1) Import modules
import os # system functions
os.system('clear')
import nipype.interfaces.dcm2nii as dcm2nii
import nipype.interfaces.io as nio # Data i/o
import nipype.interfaces.fsl as fsl # fsl
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import nipype.interfaces.fsl.utils as fslu
import nipype.interfaces.fsl.preprocess as fslp
from nipype.interfaces import afni as afni
from nipype.interfaces.utility import Function
import matplotlib
from nilearn import plotting
from nilearn import image
import os
import nipype.interfaces.fsl as fsl # fsl
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import nipype.interfaces.freesurfer as fs # freesurfer
tolist = lambda x: [x]
highpass_operand = lambda x:'-bptf %.10f -1'%x
#--- 2) Prompt user for directory containing DICOM FILES
INITDIR=os.getcwd();
#--- 3) Prompt user for inputs.
DICOMDIR=raw_input('Please drag in the directory of\nDICOM files you wish to pre-process\n(ensure there is no blank space at the end)\n')
os.system('clear')
print ('---\n')
DICOMDIR=DICOMDIR.strip('\'"')
frac=float(input('Please enter the fractional anisotropy threshold [0 - 1] \n'))
os.system('clear')
print ('---\n')
grad=float(input('Please enter the threshold gradient [-1 - 1] \n'))
os.system('clear')
print ('---\n')
FWHM=float(input('Please enter the FWHM of the smoother (mm) \n'))
os.system('clear')
print ('---\n')
HIGHPASS=float(input('Please enter the High Pass filter cutoff (s)\n'))
os.system('clear')
print ('---\n')
TR=float(input('Please enter the TR (s)\n'))
os.system('clear')
print ('---\n')
#--- 4) Define workflow and input node.
workflow = pe.Workflow(name='FUNCPIPE')
inputnode = pe.Node(interface=util.IdentityInterface(fields=['fwhm','highpass','TR']),name='inputspec')
inputnode.inputs.fwhm=FWHM
inputnode.inputs.TR=TR
inputnode.inputs.highpass=float(HIGHPASS/(inputnode.inputs.TR*2.5))
#--- 5) Move to directory
os.chdir(DICOMDIR)
#--- 6) Set up converter node for conversion to nifti
converter=pe.Node(interface=dcm2nii.Dcm2nii(),name='CONVERTED')
converter.inputs.source_dir=DICOMDIR
converter.inputs.gzip_output=bool(1)
#--- 7) Set up realigner node to match orientation of MNI 152
realigner=pe.Node(interface=fslu.Reorient2Std(),name='REORIENTED')
realigner.inputs.output_type='NIFTI_GZ'
workflow.connect(converter,'converted_files',realigner,'in_file')
#--- 8) Set up a slice timing node
slicetimer=pe.Node(interface=fslp.SliceTimer(),name='SLICETIMED')
slicetimer.inputs.interleaved = True
workflow.connect(inputnode, 'TR', slicetimer, 'time_repetition')
workflow.connect(realigner, 'out_file', slicetimer, 'in_file')
#--- 9) Convert to float.
img2float = pe.Node(interface=fsl.ImageMaths(out_data_type='float',op_string='',suffix='_dtype'),name='IMG2FLOATED')
workflow.connect(slicetimer,'slice_time_corrected_file',img2float,'in_file')
#--- 10) Motion correct.
motion_correct = pe.Node(interface=fsl.MCFLIRT(save_mats=True,save_plots=True,interpolation='spline'),name='MCORRECTED')
workflow.connect(img2float, 'out_file', motion_correct, 'in_file')
#--- 11) Despike
despiker=pe.Node(interface=afni.Despike(),name='DESPIKED')
despiker.inputs.outputtype = 'NIFTI_GZ'
workflow.connect(motion_correct,'out_file',despiker,'in_file')
#--- 12) Plot motion.
plot_motion = pe.Node(interface=fsl.PlotMotionParams(in_source='fsl'),name='MOTIONPLOTTED')
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
workflow.connect(motion_correct, 'par_file', plot_motion, 'in_file')
#--- 13) Extract
extracter=pe.Node(interface=fsl.BET(),name='EXTRACTED')
extracter.inputs.frac=float(frac)
extracter.inputs.vertical_gradient=float(grad)
extracter.inputs.mask=bool(1)
extracter.inputs.functional=bool(1)
workflow.connect(despiker, 'out_file', extracter, 'in_file')
#--- 14) Smooth
smoother=pe.MapNode(interface=afni.BlurInMask(),name='SMOOTHED',iterfield=['fwhm'])
smoother.inputs.outputtype='NIFTI_GZ'
workflow.connect(inputnode, 'fwhm', smoother, 'fwhm')
workflow.connect(extracter, 'out_file', smoother, 'in_file')
workflow.connect(extracter, 'mask_file', smoother, 'mask')
#--- 15) Highpass filter
# Filtering node
highpass = pe.MapNode(interface=fsl.ImageMaths(suffix='_tempfilt'),name='HIGHPASSED',iterfield=['in_file'])
workflow.connect(inputnode, ('highpass', highpass_operand), highpass, 'op_string')
workflow.connect(smoother, 'out_file', highpass, 'in_file')
#--- 16) Mean functional volume
# Need to add back the mean removed by FSL
meanfunc = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',suffix='_mean'),name='meanfunc',iterfield=['in_file'])
workflow.connect(smoother, 'out_file', meanfunc, 'in_file')
#--- 17) Add mean back to highpassed data (FINAL OUTPUT)
addmean = pe.MapNode(interface=fsl.BinaryMaths(operation='add'),name='PREPROCESSED',iterfield=['in_file','operand_file'])
workflow.connect(highpass, 'out_file', addmean, 'in_file')
workflow.connect(meanfunc, 'out_file', addmean, 'operand_file')
outputnode = pe.Node(interface=util.IdentityInterface(fields=['highpassed_files']),name='outputnode')
workflow.connect(addmean, 'out_file', outputnode, 'highpassed_files')
# Utility function for plotting extraction
def bplot(in_file,in_file2,in_file3):
from nilearn import image
from nilearn import plotting
import matplotlib
niftifiledim=len(image.load_img(in_file).shape)
firstim=image.index_img(in_file, 0)
firstim2=image.index_img(in_file2, 0)
display=plotting.plot_anat(firstim2)
display.add_contours(firstim,filled=True, alpha=0.5,levels=[0.2], colors='b')
display.add_edges(in_file3)
matplotlib.pyplot.show()
return niftifiledim
#--- 18) Show extraction
showextract= pe.Node(Function(input_names=['in_file','in_file2','in_file3'],output_names=['niftifiledim'],function=bplot),name='SHOWEXTRACT')
workflow.connect(despiker,'out_file', showextract,'in_file2')
workflow.connect(extracter,'out_file', showextract,'in_file')
workflow.connect(extracter,'mask_file', showextract,'in_file3')
# Utility function for plotting extraction
def splot(in_file):
from nilearn import image
from nilearn import plotting
import matplotlib
niftifiledim=len(image.load_img(in_file).shape)
firstim=image.index_img(in_file, 0)
display=plotting.plot_anat(firstim,display_mode='z',cut_coords=10)
matplotlib.pyplot.show()
return niftifiledim
#--- 19) Show smoothing
showsmooth= pe.MapNode(Function(input_names=['in_file'],output_names=['niftifiledim'],function=splot),iterfield=['in_file'],name='SHOWSMOOTH')
workflow.connect(smoother,'out_file', showsmooth,'in_file')
#--- 20) Mean functional volume (for plotting stats)
meanfunc2 = pe.Node(interface=fsl.ImageMaths(op_string='-Tmean',suffix='_mean'),name='MEANFUNCTIONAL')
workflow.connect(extracter, 'out_file', meanfunc2, 'in_file')
workflow.connect(meanfunc2, 'out_file', outputnode, 'mean_functional_volume')
#--- 21) Plot workflow
workflow.base_dir = DICOMDIR
workflow.write_graph(graph2use='exec')
#--- 22) Plot workflow
result=workflow.run()
#--- 23) Show plots
#--- 24) Return to initial working directory
print ("Workflow completed. Returning to intital directory\n")
os.chdir(INITDIR)
realign_flow = Workflow(name='realign_flow')
realign_inputnode = Node(IdentityInterface(fields=['func']), name='inputspec')
realign_outputnode = Node(IdentityInterface(fields=[
'realigned_file', 'transformation_matrices', 'motion_parameters',
'displacement_parameters', 'motion_plots'
]),
name='outputspec')
realigner = Node(fsl.MCFLIRT(save_mats=True, stats_imgs=True, save_plots=True),
name='realigner')
splitter = Node(fsl.Split(dimension='t'), name='splitter')
warper = MapNode(fsl.ApplyWarp(interp='spline'),
iterfield=['in_file', 'premat'],
name='warper')
joiner = Node(fsl.Merge(dimension='t'), name='joiner')
plot_motion = Node(fsl.PlotMotionParams(in_source='fsl'), name='plot_motion')
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
realign_flow.connect(realign_inputnode, 'func', realigner, 'in_file')
realign_flow.connect(realign_inputnode, ('func', select_volume, 'middle'),
realigner, 'ref_vol')
realign_flow.connect(realigner, 'out_file', splitter, 'in_file')
realign_flow.connect(realigner, 'mat_file', warper, 'premat')
realign_flow.connect(realigner, 'variance_img', warper, 'ref_file')
realign_flow.connect(realigner, 'par_file', plot_motion, 'in_file')
realign_flow.connect(splitter, 'out_files', warper, 'in_file')
realign_flow.connect(warper, 'out_file', joiner, 'in_files')
realign_flow.connect(joiner, 'merged_file', realign_outputnode,
'realigned_file')
realign_flow.connect(realigner, 'mat_file', realign_outputnode,
'transformation_matrices')
def func_preproc_fsl(wf_name='func_preproc'):
featpreproc = pe.Workflow(name=wf_name)
"""
Set up a node to define all inputs required for the preprocessing workflow
"""
inputnode = pe.Node(interface=util.IdentityInterface(
fields=['in_file', 'anat_brain'], mandatory_inputs=True),
name='inputspec')
# preprocessed_func: upscaled, brain-extracted and motion corrected functional data
outputnode = pe.Node(interface=util.IdentityInterface(
fields=[
'preprocessed_func', 'example_func', 'func_brain_mask',
'motion_plots', 'func2anat_mat'
],
mandatory_inputs=True),
name='outputspec')
"""
Reorient data to match Paxinos
"""
reorient = pe.MapNode(interface=fsl.utils.SwapDimensions(new_dims=("RL",
"AP",
"IS")),
name='reorient',
iterfield=['in_file'])
featpreproc.connect(inputnode, 'in_file', reorient, 'in_file')
"""
Upscale data to human range
"""
upscaler = mine.upscale()
featpreproc.connect(reorient, 'out_file', upscaler, 'inputspec.in_file')
"""
Convert functional images to float representation. Since there can
be more than one functional run we use a MapNode to convert each
run.
"""
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
featpreproc.connect(upscaler, 'outputspec.out_file', img2float, 'in_file')
"""
Extract the first volume of the first run as the reference
"""
extract_ref = pe.MapNode(interface=fsl.ExtractROI(t_size=1),
iterfield=['in_file', 't_min'],
name='extractref')
featpreproc.connect(img2float, 'out_file', extract_ref, 'in_file')
featpreproc.connect(img2float, ('out_file', pickmiddle), extract_ref,
't_min')
featpreproc.connect(extract_ref, 'roi_file', outputnode, 'example_func')
"""
Realign the functional runs to the reference (1st volume of first run)
"""
motion_correct = pe.MapNode(interface=fsl.MCFLIRT(save_mats=True,
save_plots=True),
name='motioncorr',
iterfield=['in_file', 'ref_file'])
featpreproc.connect(img2float, 'out_file', motion_correct, 'in_file')
featpreproc.connect(extract_ref, 'roi_file', motion_correct, 'ref_file')
featpreproc.connect(motion_correct, 'par_file', outputnode,
'motion_parameters')
featpreproc.connect(motion_correct, 'out_file', outputnode,
'realigned_files')
"""
Plot the estimated motion parameters
"""
plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
plot_motion.iterables = ('plot_type',
['displacement', 'rotations', 'translations'])
featpreproc.connect(motion_correct, 'par_file', plot_motion, 'in_file')
featpreproc.connect(plot_motion, 'out_file', outputnode, 'motion_plots')
"""
Extract the mean volume of the first functional run
"""
meanfunc = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc')
featpreproc.connect(motion_correct, 'out_file', meanfunc, 'in_file')
"""
estimate func2anat matrix
"""
f2a = pe.MapNode(util.Function(input_names=['in_file', 'like'],
output_names=['out_mat'],
function=myfsl.utils.run_resample),
name='func2anat',
iterfield=['in_file', 'like'])
featpreproc.connect(meanfunc, 'out_file', f2a, 'in_file')
featpreproc.connect(inputnode, 'anat_brain', f2a, 'like')
featpreproc.connect(f2a, 'out_mat', outputnode, 'func2anat_mat')
"""
Invert func2anat matrix
"""
invertmat = pe.MapNode(interface=fsl.ConvertXFM(invert_xfm=True),
iterfield=['in_file'],
name='invertmat')
featpreproc.connect(f2a, 'out_mat', invertmat, 'in_file')
"""
Resample the anatomical brain mask to the space of functional image
"""
resamplemask = pe.MapNode(
interface=fsl.ApplyXfm(interp='nearestneighbour'),
iterfield=['reference', 'in_file', 'in_matrix_file'],
name='resamplemask')
featpreproc.connect(inputnode, 'anat_brain', resamplemask, 'in_file')
featpreproc.connect(meanfunc, 'out_file', resamplemask, 'reference')
featpreproc.connect(invertmat, 'out_file', resamplemask, 'in_matrix_file')
"""
Mask the functional runs with the resampled mask
"""
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc')
featpreproc.connect(motion_correct, 'out_file', maskfunc, 'in_file')
featpreproc.connect(resamplemask, 'out_file', maskfunc, 'in_file2')
"""
Determine the 2nd and 98th percentile intensities of each functional run
"""
getthresh = pe.MapNode(interface=fsl.ImageStats(op_string='-p 2 -p 98'),
iterfield=['in_file'],
name='getthreshold')
featpreproc.connect(maskfunc, 'out_file', getthresh, 'in_file')
"""
Threshold the first run of the functional data at 10% of the 98th percentile
"""
threshold = pe.MapNode(interface=fsl.ImageMaths(out_data_type='char',
suffix='_thresh'),
iterfield=['in_file', 'op_string'],
name='threshold')
featpreproc.connect(maskfunc, 'out_file', threshold, 'in_file')
"""
Define a function to get 10% of the intensity
"""
featpreproc.connect(getthresh, ('out_stat', getthreshop), threshold,
'op_string')
featpreproc.connect(threshold, 'out_file', outputnode, 'func_brain_mask')
#"""
#Determine the median value of the functional runs using the mask
#"""
#medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
# iterfield=['in_file', 'mask_file'],
# name='medianval')
#featpreproc.connect(motion_correct, 'out_file', medianval, 'in_file')
#featpreproc.connect(threshold, 'out_file', medianval, 'mask_file')
#"""
#Dilate the mask
#"""
#dilatemask = pe.MapNode(interface=fsl.ImageMaths(suffix='_dil',
# op_string='-dilF'),
# iterfield=['in_file'],
# name='dilatemask')
#featpreproc.connect(threshold, 'out_file', dilatemask, 'in_file')
"""
Mask the motion corrected functional runs with the dilated mask
"""
maskfunc2 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc2')
featpreproc.connect(motion_correct, 'out_file', maskfunc2, 'in_file')
featpreproc.connect(threshold, 'out_file', maskfunc2, 'in_file2')
#featpreproc.connect(dilatemask, 'out_file', maskfunc2, 'in_file2')
featpreproc.connect(maskfunc2, 'out_file', outputnode, 'preprocessed_func')
return featpreproc
def mc_workflow_fsl(reference_vol="mid",
FD_mode="Power",
SinkTag="func_preproc",
wf_name="motion_correction_fsl"):
"""
Modified version of CPAC.func_preproc.func_preproc and CPAC.generate_motion_statistics.generate_motion_statistics:
`source: https://fcp-indi.github.io/docs/developer/_modules/CPAC/func_preproc/func_preproc.html`
`source: https://fcp-indi.github.io/docs/developer/_modules/CPAC/generate_motion_statistics/generate_motion_statistics.html`
Use FSL MCFLIRT to do the motion correction of the 4D functional data and use the 6df rigid body motion parameters to calculate friston24 parameters
for later nuissance regression step.
Workflow inputs:
:param func: The reoriented functional file.
:param reference_vol: Either "first", "mid", "last", "mean", or the index of the volume which the rigid body registration (motion correction) will use as reference.
default: "mid"
:param FD_mode Eiher "Power" or "Jenkinson"
:param SinkDir:
:param SinkTag: The output directory in which the returned images (see workflow outputs) could be found in a subdirectory directory specific for this workflow..
Workflow outputs:
:return: mc_workflow - workflow
Balint Kincses
[email protected]
2018
"""
# TODO_ready nipype has the ability to calculate FD: the function from CPAC calculates it correctly
# import relevant packages
import sys
import os
import nipype
import nipype.pipeline as pe
import nipype.interfaces.utility as utility
import nipype.interfaces.fsl as fsl
import nipype.algorithms.confounds as conf
import PUMI.func_preproc.info.info_get as info_get
import nipype.interfaces.io as io
import PUMI.utils.utils_math as utils_math
import PUMI.utils.utils_convert as utils_convert
import PUMI.utils.globals as globals
import PUMI.utils.QC as qc
SinkDir = os.path.abspath(globals._SinkDir_ + "/" + SinkTag)
if not os.path.exists(SinkDir):
os.makedirs(SinkDir)
QCDir = os.path.abspath(globals._SinkDir_ + "/" + globals._QCDir_)
if not os.path.exists(QCDir):
os.makedirs(QCDir)
# Basic interface class generates identity mappings
inputspec = pe.Node(utility.IdentityInterface(
fields=['func', 'ref_vol', 'save_plots', 'stats_imgs']),
name='inputspec')
inputspec.inputs.save_plots = True
inputspec.inputs.stats_imgs = True
inputspec.inputs.ref_vol = reference_vol
# todo_ready: make parametrizable: the reference_vol variable is an argumentum of the mc_workflow
# extract reference volume
refvol = pe.MapNode(utility.Function(input_names=['refvol', 'func'],
output_names=['refvol'],
function=getRefVol),
iterfield=['func'],
name='getRefVol')
# Wraps command **mcflirt**
mcflirt = pe.MapNode(
interface=fsl.MCFLIRT(
interpolation="spline",
stats_imgs=False), # stages=4), #stages 4: more accurate but slow
iterfield=['in_file',
'ref_file'], # , 'ref_vol'], # make parametrizable
name='mcflirt')
if (reference_vol == "mean"):
mcflirt = pe.MapNode(
interface=fsl.MCFLIRT(interpolation="spline", stats_imgs=False),
# stages=4), #stages 4: more accurate but slow
iterfield=['in_file'], # , 'ref_vol'], # make parametrizable
name='mcflirt')
mcflirt.inputs.mean_vol = True
else:
mcflirt = pe.MapNode(
interface=fsl.MCFLIRT(interpolation="spline", stats_imgs=False),
# stages=4), #stages 4: more accurate but slow
iterfield=['in_file',
'ref_file'], # , 'ref_vol'], # make parametrizable
name='mcflirt')
mcflirt.inputs.dof = 6
mcflirt.inputs.save_mats = True
mcflirt.inputs.save_plots = True
mcflirt.inputs.save_rms = True
mcflirt.inputs.stats_imgs = False
myqc = qc.timecourse2png("timeseries", tag="010_motioncorr")
# Calculate Friston24 parameters
calc_friston = pe.MapNode(utility.Function(
input_names=['in_file'],
output_names=['out_file'],
function=calc_friston_twenty_four),
iterfield=['in_file'],
name='calc_friston')
# Calculate FD based on Power's method
if FD_mode == "Power":
calculate_FD = pe.MapNode(conf.FramewiseDisplacement(
parameter_source='FSL', save_plot=True),
iterfield=['in_file'],
name='calculate_FD_Power')
elif FD_mode == "Jenkinson":
calculate_FD = pe.MapNode(utility.Function(input_names=['in_file'],
output_names=['out_file'],
function=calculate_FD_J),
iterfield=['in_file'],
name='calculate_FD_Jenkinson')
# compute mean and max FD
meanFD = pe.MapNode(interface=utils_math.Txt2meanTxt,
iterfield=['in_file'],
name='meanFD')
meanFD.inputs.axis = 0 # global mean
meanFD.inputs.header = True # global mean
maxFD = pe.MapNode(interface=utils_math.Txt2maxTxt,
iterfield=['in_file'],
name='maxFD')
maxFD.inputs.axis = 0 # global mean
maxFD.inputs.header = True
pop_FD = pe.Node(interface=utils_convert.List2TxtFileOpen, name='pop_FD')
pop_FDmax = pe.Node(interface=utils_convert.List2TxtFileOpen,
name='pop_FDmax')
# save data out with Datasink
ds_fd = pe.Node(interface=io.DataSink(), name='ds_pop_fd')
ds_fd.inputs.regexp_substitutions = [("(\/)[^\/]*$", "FD.txt")]
ds_fd.inputs.base_directory = SinkDir
# save data out with Datasink
ds_fd_max = pe.Node(interface=io.DataSink(), name='ds_pop_fd_max')
ds_fd_max.inputs.regexp_substitutions = [("(\/)[^\/]*$", "FD_max.txt")]
ds_fd_max.inputs.base_directory = SinkDir
plot_motion_rot = pe.MapNode(
interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion_rot',
iterfield=['in_file'])
plot_motion_rot.inputs.plot_type = 'rotations'
plot_motion_tra = pe.MapNode(
interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion_trans',
iterfield=['in_file'])
plot_motion_tra.inputs.plot_type = 'translations'
# Basic interface class generates identity mappings
outputspec = pe.Node(utility.IdentityInterface(fields=[
'func_out_file', 'first24_file', 'mat_file', 'mc_par_file', 'FD_file'
]),
name='outputspec')
# save data out with Datasink
ds_nii = pe.Node(interface=io.DataSink(), name='ds_nii')
ds_nii.inputs.regexp_substitutions = [("(\/)[^\/]*$", ".nii.gz")]
ds_nii.inputs.base_directory = SinkDir
# save data out with Datasink
ds_text = pe.Node(interface=io.DataSink(), name='ds_txt')
ds_text.inputs.regexp_substitutions = [("(\/)[^\/]*$", ".txt")]
ds_text.inputs.base_directory = SinkDir
# Save outputs which are important
ds_qc_fd = pe.Node(interface=io.DataSink(), name='ds_qc_fd')
ds_qc_fd.inputs.base_directory = QCDir
ds_qc_fd.inputs.regexp_substitutions = [("(\/)[^\/]*$", "_FD.pdf")]
# Save outputs which are important
ds_qc_rot = pe.Node(interface=io.DataSink(), name='ds_qc_rot')
ds_qc_rot.inputs.base_directory = QCDir
ds_qc_rot.inputs.regexp_substitutions = [("(\/)[^\/]*$", "_rot.png")]
# Save outputs which are important
ds_qc_tra = pe.Node(interface=io.DataSink(), name='ds_qc_tra')
ds_qc_tra.inputs.base_directory = QCDir
ds_qc_tra.inputs.regexp_substitutions = [("(\/)[^\/]*$", "_trans.png")]
#TODO_ready set the proper images which has to be saved in a the datasink specified directory
# Create a workflow to connect all those nodes
analysisflow = nipype.Workflow(wf_name)
analysisflow.connect(inputspec, 'func', mcflirt, 'in_file')
analysisflow.connect(inputspec, 'func', refvol, 'func')
analysisflow.connect(inputspec, 'ref_vol', refvol, 'refvol')
if (reference_vol != "mean"):
analysisflow.connect(refvol, 'refvol', mcflirt, 'ref_file')
analysisflow.connect(mcflirt, 'par_file', calc_friston, 'in_file')
analysisflow.connect(mcflirt, 'par_file', calculate_FD, 'in_file')
analysisflow.connect(mcflirt, 'out_file', outputspec, 'func_out_file')
analysisflow.connect(mcflirt, 'mat_file', outputspec, 'mat_file')
analysisflow.connect(mcflirt, 'par_file', outputspec, 'mc_par_file')
analysisflow.connect(mcflirt, 'out_file', ds_nii, 'mc_func')
analysisflow.connect(mcflirt, 'par_file', ds_text, 'mc_par')
#analysisflow.connect(mcflirt, 'std_img', ds, 'mc.@std_img')
analysisflow.connect(mcflirt, 'rms_files', ds_text, 'mc_rms')
#analysisflow.connect(mcflirt, 'variance_img', ds, 'mc.@variance_img')
analysisflow.connect(calc_friston, 'out_file', outputspec, 'first24_file')
analysisflow.connect(calc_friston, 'out_file', ds_text, 'mc_first24')
analysisflow.connect(calculate_FD, 'out_file', outputspec, 'FD_file')
analysisflow.connect(mcflirt, 'par_file', plot_motion_rot, 'in_file')
analysisflow.connect(mcflirt, 'par_file', plot_motion_tra, 'in_file')
analysisflow.connect(plot_motion_rot, 'out_file', ds_qc_rot,
'motion_correction')
analysisflow.connect(plot_motion_tra, 'out_file', ds_qc_tra,
'motion_correction')
analysisflow.connect(mcflirt, 'out_file', myqc, 'inputspec.func')
# pop-level mean FD
analysisflow.connect(calculate_FD, 'out_file', meanFD, 'in_file')
analysisflow.connect(calculate_FD, 'out_file', ds_text, 'mc_fd')
analysisflow.connect(calculate_FD, 'out_figure', ds_qc_fd, 'FD')
analysisflow.connect(meanFD, 'mean_file', pop_FD, 'in_list')
analysisflow.connect(pop_FD, 'txt_file', ds_fd, 'pop')
analysisflow.connect(calculate_FD, 'out_file', maxFD, 'in_file')
analysisflow.connect(maxFD, 'max_file', pop_FDmax, 'in_list')
analysisflow.connect(pop_FDmax, 'txt_file', ds_fd_max, 'pop')
return analysisflow
def create_fsl_fs_preproc(name='preproc', highpass=True, whichvol='middle'):
"""Create a FEAT preprocessing workflow together with freesurfer
Parameters
----------
::
name : name of workflow (default: preproc)
highpass : boolean (default: True)
whichvol : which volume of the first run to register to ('first', 'middle', 'mean')
Inputs::
inputspec.func : functional runs (filename or list of filenames)
inputspec.fwhm : fwhm for smoothing with SUSAN
inputspec.highpass : HWHM in TRs (if created with highpass=True)
inputspec.subject_id : freesurfer subject id
inputspec.subjects_dir : freesurfer subjects dir
Outputs::
outputspec.reference : volume to which runs are realigned
outputspec.motion_parameters : motion correction parameters
outputspec.realigned_files : motion corrected files
outputspec.motion_plots : plots of motion correction parameters
outputspec.mask_file : mask file used to mask the brain
outputspec.smoothed_files : smoothed functional data
outputspec.highpassed_files : highpassed functional data (if highpass=True)
outputspec.reg_file : bbregister registration files
outputspec.reg_cost : bbregister registration cost files
Example
-------
>>> preproc = create_fsl_fs_preproc(whichvol='first')
>>> preproc.inputs.inputspec.highpass = 128./(2*2.5)
>>> preproc.inputs.inputspec.func = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.subjects_dir = '.'
>>> preproc.inputs.inputspec.subject_id = 's1'
>>> preproc.inputs.inputspec.fwhm = 6
>>> preproc.run() # doctest: +SKIP
"""
featpreproc = pe.Workflow(name=name)
"""
Set up a node to define all inputs required for the preprocessing workflow
"""
if highpass:
inputnode = pe.Node(interface=util.IdentityInterface(fields=['func',
'fwhm',
'subject_id',
'subjects_dir',
'highpass']),
name='inputspec')
outputnode = pe.Node(interface=util.IdentityInterface(fields=['reference',
'motion_parameters',
'realigned_files',
'motion_plots',
'mask_file',
'smoothed_files',
'highpassed_files',
'reg_file',
'reg_cost'
]),
name='outputspec')
else:
inputnode = pe.Node(interface=util.IdentityInterface(fields=['func',
'fwhm',
'subject_id',
'subjects_dir'
]),
name='inputspec')
outputnode = pe.Node(interface=util.IdentityInterface(fields=['reference',
'motion_parameters',
'realigned_files',
'motion_plots',
'mask_file',
'smoothed_files',
'reg_file',
'reg_cost'
]),
name='outputspec')
"""
Set up a node to define outputs for the preprocessing workflow
"""
"""
Convert functional images to float representation. Since there can
be more than one functional run we use a MapNode to convert each
run.
"""
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string = '',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
featpreproc.connect(inputnode, 'func', img2float, 'in_file')
"""
Extract the first volume of the first run as the reference
"""
if whichvol != 'mean':
extract_ref = pe.Node(interface=fsl.ExtractROI(t_size=1),
iterfield=['in_file'],
name = 'extractref')
featpreproc.connect(img2float, ('out_file', pickfirst), extract_ref, 'in_file')
featpreproc.connect(img2float, ('out_file', pickvol, 0, whichvol), extract_ref, 't_min')
featpreproc.connect(extract_ref, 'roi_file', outputnode, 'reference')
"""
Realign the functional runs to the reference (1st volume of first run)
"""
motion_correct = pe.MapNode(interface=fsl.MCFLIRT(save_mats = True,
save_plots = True,
interpolation = 'sinc'),
name='realign',
iterfield = ['in_file'])
featpreproc.connect(img2float, 'out_file', motion_correct, 'in_file')
if whichvol != 'mean':
featpreproc.connect(extract_ref, 'roi_file', motion_correct, 'ref_file')
else:
motion_correct.inputs.mean_vol = True
featpreproc.connect(motion_correct, 'mean_img', outputnode, 'reference')
featpreproc.connect(motion_correct, 'par_file', outputnode, 'motion_parameters')
featpreproc.connect(motion_correct, 'out_file', outputnode, 'realigned_files')
"""
Plot the estimated motion parameters
"""
plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
featpreproc.connect(motion_correct, 'par_file', plot_motion, 'in_file')
featpreproc.connect(plot_motion, 'out_file', outputnode, 'motion_plots')
"""Get the mask from subject for each run
"""
maskflow = create_getmask_flow()
featpreproc.connect([(inputnode, maskflow, [('subject_id','inputspec.subject_id'),
('subjects_dir', 'inputspec.subjects_dir')])])
maskflow.inputs.inputspec.contrast_type = 't2'
if whichvol != 'mean':
featpreproc.connect(extract_ref, 'roi_file', maskflow, 'inputspec.source_file')
else:
featpreproc.connect(motion_correct, ('mean_img', pickfirst), maskflow, 'inputspec.source_file')
"""
Mask the functional runs with the extracted mask
"""
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file'],
name = 'maskfunc')
featpreproc.connect(motion_correct, 'out_file', maskfunc, 'in_file')
featpreproc.connect(maskflow, ('outputspec.mask_file', pickfirst), maskfunc, 'in_file2')
"""
Smooth each run using SUSAN with the brightness threshold set to 75%
of the median value for each run and a mask consituting the mean
functional
"""
smooth = create_susan_smooth(separate_masks=False)
featpreproc.connect(inputnode, 'fwhm', smooth, 'inputnode.fwhm')
featpreproc.connect(maskfunc, 'out_file', smooth, 'inputnode.in_files')
featpreproc.connect(maskflow, ('outputspec.mask_file', pickfirst), smooth, 'inputnode.mask_file')
"""
Mask the smoothed data with the dilated mask
"""
maskfunc3 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file'],
name='maskfunc3')
featpreproc.connect(smooth, 'outputnode.smoothed_files', maskfunc3, 'in_file')
featpreproc.connect(maskflow, ('outputspec.mask_file', pickfirst), maskfunc3, 'in_file2')
concatnode = pe.Node(interface=util.Merge(2),
name='concat')
featpreproc.connect(maskfunc, ('out_file', tolist), concatnode, 'in1')
featpreproc.connect(maskfunc3, ('out_file', tolist), concatnode, 'in2')
"""
The following nodes select 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.
"""
selectnode = pe.Node(interface=util.Select(),name='select')
featpreproc.connect(concatnode, 'out', selectnode, 'inlist')
featpreproc.connect(inputnode, ('fwhm', chooseindex), selectnode, 'index')
featpreproc.connect(selectnode, 'out', outputnode, 'smoothed_files')
"""
Scale the median value of the run is set to 10000
"""
meanscale = pe.MapNode(interface=fsl.ImageMaths(suffix='_gms'),
iterfield=['in_file','op_string'],
name='meanscale')
featpreproc.connect(selectnode, 'out', meanscale, 'in_file')
"""
Determine the median value of the functional runs using the mask
"""
medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
iterfield = ['in_file'],
name='medianval')
featpreproc.connect(motion_correct, 'out_file', medianval, 'in_file')
featpreproc.connect(maskflow, ('outputspec.mask_file', pickfirst), medianval, 'mask_file')
"""
Define a function to get the scaling factor for intensity normalization
"""
featpreproc.connect(medianval, ('out_stat', getmeanscale), meanscale, 'op_string')
"""
Perform temporal highpass filtering on the data
"""
if highpass:
highpass = pe.MapNode(interface=fsl.ImageMaths(suffix='_tempfilt'),
iterfield=['in_file'],
name='highpass')
featpreproc.connect(inputnode, ('highpass', highpass_operand), highpass, 'op_string')
featpreproc.connect(meanscale, 'out_file', highpass, 'in_file')
featpreproc.connect(highpass, 'out_file', outputnode, 'highpassed_files')
featpreproc.connect(maskflow, ('outputspec.mask_file', pickfirst), outputnode, 'mask_file')
featpreproc.connect(maskflow, 'outputspec.reg_file', outputnode, 'reg_file')
featpreproc.connect(maskflow, 'outputspec.reg_cost', outputnode, 'reg_cost')
return featpreproc
def create_moco_pipeline(working_dir, ds_dir, name='motion_correction'):
"""
Workflow for motion correction to 1st volume
based on https://github.com/NeuroanatomyAndConnectivity/pipelines/blob/master/src/lsd_lemon/func_preproc/moco.py
"""
# initiate workflow
moco_wf = Workflow(name=name)
moco_wf.base_dir = os.path.join(working_dir, 'LeiCA_resting',
'rsfMRI_preprocessing')
# set fsl output
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# I/O NODES
inputnode = Node(util.IdentityInterface(fields=['epi', 'vols_to_drop']),
name='inputnode')
outputnode = Node(util.IdentityInterface(fields=[
'epi_moco', 'par_moco', 'mat_moco', 'rms_moco',
'initial_mean_epi_moco', 'rotplot', 'transplot', 'dispplots',
'tsnr_file', 'epi_mask'
]),
name='outputnode')
ds = Node(nio.DataSink(base_directory=ds_dir), name='ds')
ds.inputs.substitutions = [('_TR_id_', 'TR_')]
# REMOVE FIRST VOLUMES
drop_vols = Node(util.Function(input_names=['in_file', 't_min'],
output_names=['out_file'],
function=strip_rois_func),
name='remove_vol')
moco_wf.connect(inputnode, 'epi', drop_vols, 'in_file')
moco_wf.connect(inputnode, 'vols_to_drop', drop_vols, 't_min')
# MCFILRT MOCO TO 1st VOLUME
mcflirt = Node(fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
ref_vol=0,
out_file='rest_realigned.nii.gz'),
name='mcflirt')
moco_wf.connect(drop_vols, 'out_file', mcflirt, 'in_file')
moco_wf.connect([(mcflirt, ds, [('par_file', 'realign.par.@par'),
('mat_file', 'realign.MAT.@mat'),
('rms_files', 'realign.plots.@rms')])])
moco_wf.connect([(mcflirt, outputnode, [('out_file', 'epi_moco'),
('par_file', 'par_moco'),
('mat_file', 'mat_moco'),
('rms_files', 'rms_moco')])])
# CREATE MEAN EPI (INTENSITY NORMALIZED)
initial_mean_epi_moco = Node(fsl.maths.MeanImage(
dimension='T', out_file='initial_mean_epi_moco.nii.gz'),
name='initial_mean_epi_moco')
moco_wf.connect(mcflirt, 'out_file', initial_mean_epi_moco, 'in_file')
moco_wf.connect(initial_mean_epi_moco, 'out_file', outputnode,
'initial_mean_epi_moco')
moco_wf.connect(initial_mean_epi_moco, 'out_file', ds,
'QC.initial_mean_epi_moco')
# PLOT MOTION PARAMETERS
rotplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='rotations',
out_file='rotation_plot.png'),
name='rotplotter')
moco_wf.connect(mcflirt, 'par_file', rotplotter, 'in_file')
moco_wf.connect(rotplotter, 'out_file', ds, 'realign.plots.@rotplot')
transplotter = Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='translations',
out_file='translation_plot.png'),
name='transplotter')
moco_wf.connect(mcflirt, 'par_file', transplotter, 'in_file')
moco_wf.connect(transplotter, 'out_file', ds, 'realign.plots.@transplot')
dispplotter = MapNode(interface=fsl.PlotMotionParams(
in_source='fsl', plot_type='displacement'),
name='dispplotter',
iterfield=['in_file'])
dispplotter.iterables = ('plot_type', ['displacement'])
moco_wf.connect(mcflirt, 'rms_files', dispplotter, 'in_file')
moco_wf.connect(dispplotter, 'out_file', ds, 'realign.plots.@dispplots')
moco_wf.write_graph(dotfilename=moco_wf.name,
graph2use='flat',
format='pdf')
return moco_wf
#Wraps command **flirt**
NodeHash_8f61130 = pe.MapNode(interface = fsl.FLIRT(), name = 'NodeName_8f61130', iterfield = ['in_file', 'in_matrix_file', 'reference', 'wm_seg'])
NodeHash_8f61130.inputs.cost = 'bbr'
NodeHash_8f61130.inputs.dof = 6
NodeHash_8f61130.inputs.no_resample = True
#Wraps command **mcflirt**
NodeHash_c3ef3c0 = pe.MapNode(interface = fsl.MCFLIRT(), name = 'NodeName_c3ef3c0', iterfield = ['in_file', 'ref_file'])
NodeHash_c3ef3c0.inputs.interpolation = 'spline'
NodeHash_c3ef3c0.inputs.save_mats = True
NodeHash_c3ef3c0.inputs.save_plots = True
NodeHash_c3ef3c0.inputs.save_rms = True
#Wraps command **fsl_tsplot**
NodeHash_c4a9c30 = pe.MapNode(interface = fsl.PlotMotionParams(), name = 'NodeName_c4a9c30', iterfield = ['in_file'])
NodeHash_c4a9c30.inputs.args = '-a x,y,z -w 640 -h 144'
NodeHash_c4a9c30.inputs.in_source = 'fsl'
NodeHash_c4a9c30.iterables = [('plot_type', ['rotations', 'translations'])]
#Wraps command **fslmaths**
NodeHash_1040c610 = pe.MapNode(interface = fsl.MeanImage(), name = 'NodeName_1040c610', iterfield = ['in_file'])
NodeHash_1040c610.inputs.dimension = 'T'
#Wraps command **bet**
NodeHash_1212d0d0 = pe.MapNode(interface = fsl.BET(), name = 'NodeName_1212d0d0', iterfield = ['in_file'])
NodeHash_1212d0d0.inputs.frac = 0.3
NodeHash_1212d0d0.inputs.mask = True
NodeHash_1212d0d0.inputs.no_output = True
#Wraps command **fslmaths**
def create_motion_correction_workflow(name='moco',
method='AFNI',
extend_moco_params=False):
"""uses sub-workflows to perform different registration steps.
Requires fsl and freesurfer tools
Parameters
----------
name : string
name of workflow
Example
-------
>>> motion_correction_workflow = create_motion_correction_workflow('motion_correction_workflow')
>>> motion_correction_workflow.inputs.inputspec.output_directory = '/data/project/raw/BIDS/sj_1/'
>>> motion_correction_workflow.inputs.inputspec.in_files = ['sub-001.nii.gz','sub-002.nii.gz']
>>> motion_correction_workflow.inputs.inputspec.which_file_is_EPI_space = 'middle'
Inputs::
inputspec.output_directory : directory in which to sink the result files
inputspec.in_files : list of functional files
inputspec.which_file_is_EPI_space : determines which file is the 'standard EPI space'
Outputs::
outputspec.EPI_space_file : standard EPI space file, one timepoint
outputspec.motion_corrected_files : motion corrected files
outputspec.motion_correction_plots : motion correction plots
outputspec.motion_correction_parameters : motion correction parameters
"""
### NODES
input_node = pe.Node(IdentityInterface(fields=[
'in_files', 'output_directory', 'which_file_is_EPI_space', 'sub_id',
'tr'
]),
name='inputspec')
output_node = pe.Node(IdentityInterface(fields=([
'motion_corrected_files', 'EPI_space_file', 'mask_EPI_space_file',
'motion_correction_plots', 'motion_correction_parameters',
'extended_motion_correction_parameters',
'new_motion_correction_parameters'
])),
name='outputspec')
########################################################################################
# Invariant nodes
########################################################################################
EPI_file_selector_node = pe.Node(interface=EPI_file_selector,
name='EPI_file_selector_node')
mean_bold = pe.Node(interface=fsl.maths.MeanImage(dimension='T'),
name='mean_space')
rename_mean_bold = pe.Node(niu.Rename(format_string='session_EPI_space',
keep_ext=True),
name='rename_mean_bold')
########################################################################################
# Workflow
########################################################################################
motion_correction_workflow = pe.Workflow(name=name)
motion_correction_workflow.connect(input_node, 'which_file_is_EPI_space',
EPI_file_selector_node, 'which_file')
motion_correction_workflow.connect(input_node, 'in_files',
EPI_file_selector_node, 'in_files')
########################################################################################
# outputs via datasink
########################################################################################
datasink = pe.Node(nio.DataSink(), name='sinker')
datasink.inputs.parameterization = False
# first link the workflow's output_directory into the datasink.
motion_correction_workflow.connect(input_node, 'output_directory',
datasink, 'base_directory')
motion_correction_workflow.connect(input_node, 'sub_id', datasink,
'container')
########################################################################################
# FSL MCFlirt
########################################################################################
# new approach, which should aid in the joint motion correction of
# multiple sessions together, by pre-registering each run.
# the strategy would be to, for each run, take the first TR
# and FLIRT-align (6dof) it to the EPI_space file.
# then we can use this as an --infile argument to mcflirt.
if method == 'FSL':
rename_motion_files = pe.MapNode(
niu.Rename(keep_ext=False),
name='rename_motion_files',
iterfield=['in_file', 'format_string'])
remove_niigz_ext = pe.MapNode(interface=Remove_extension,
name='remove_niigz_ext',
iterfield=['in_file'])
motion_correct_EPI_space = pe.Node(interface=fsl.MCFLIRT(
cost='normcorr', interpolation='sinc', mean_vol=True),
name='motion_correct_EPI_space')
motion_correct_all = pe.MapNode(interface=fsl.MCFLIRT(
save_mats=True,
save_plots=True,
cost='normcorr',
interpolation='sinc',
stats_imgs=True),
name='motion_correct_all',
iterfield=['in_file'])
plot_motion = pe.MapNode(
interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
if extend_moco_params:
# make extend_motion_pars node here
# extend_motion_pars = pe.MapNode(Function(input_names=['moco_par_file', 'tr'], output_names=['new_out_file', 'ext_out_file'],
# function=_extend_motion_parameters), name='extend_motion_pars', iterfield = ['moco_par_file'])
pass
# create reference:
motion_correction_workflow.connect(EPI_file_selector_node, 'out_file',
motion_correct_EPI_space, 'in_file')
motion_correction_workflow.connect(motion_correct_EPI_space,
'out_file', mean_bold, 'in_file')
motion_correction_workflow.connect(mean_bold, 'out_file',
motion_correct_all, 'ref_file')
# motion correction across runs
motion_correction_workflow.connect(input_node, 'in_files',
motion_correct_all, 'in_file')
#motion_correction_workflow.connect(motion_correct_all, 'out_file', output_node, 'motion_corrected_files')
# motion_correction_workflow.connect(motion_correct_all, 'par_file', extend_motion_pars, 'moco_par_file')
# motion_correction_workflow.connect(input_node, 'tr', extend_motion_pars, 'tr')
# motion_correction_workflow.connect(extend_motion_pars, 'ext_out_file', output_node, 'extended_motion_correction_parameters')
# motion_correction_workflow.connect(extend_motion_pars, 'new_out_file', output_node, 'new_motion_correction_parameters')
########################################################################################
# Plot the estimated motion parameters
########################################################################################
# rename:
motion_correction_workflow.connect(mean_bold, 'out_file',
rename_mean_bold, 'in_file')
motion_correction_workflow.connect(motion_correct_all, 'par_file',
rename_motion_files, 'in_file')
motion_correction_workflow.connect(motion_correct_all, 'par_file',
remove_niigz_ext, 'in_file')
motion_correction_workflow.connect(remove_niigz_ext, 'out_file',
rename_motion_files,
'format_string')
# plots:
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
motion_correction_workflow.connect(rename_motion_files, 'out_file',
plot_motion, 'in_file')
motion_correction_workflow.connect(plot_motion, 'out_file',
output_node,
'motion_correction_plots')
# output node:
motion_correction_workflow.connect(mean_bold, 'out_file', output_node,
'EPI_space_file')
motion_correction_workflow.connect(rename_motion_files, 'out_file',
output_node,
'motion_correction_parameters')
motion_correction_workflow.connect(motion_correct_all, 'out_file',
output_node,
'motion_corrected_files')
# datasink:
motion_correction_workflow.connect(rename_mean_bold, 'out_file',
datasink, 'reg')
motion_correction_workflow.connect(motion_correct_all, 'out_file',
datasink, 'mcf')
motion_correction_workflow.connect(rename_motion_files, 'out_file',
datasink, 'mcf.motion_pars')
motion_correction_workflow.connect(plot_motion, 'out_file', datasink,
'mcf.motion_plots')
# motion_correction_workflow.connect(extend_motion_pars, 'ext_out_file', datasink, 'mcf.ext_motion_pars')
# motion_correction_workflow.connect(extend_motion_pars, 'new_out_file', datasink, 'mcf.new_motion_pars')
########################################################################################
# AFNI 3DVolReg
########################################################################################
# for speed, we use AFNI's 3DVolReg brute-force.
# this loses plotting of motion parameters but increases speed
# we hold on to the same setup, first moco the selected run
# and then moco everything to that image, but without the
# intermediate FLIRT step.
if method == 'AFNI':
motion_correct_EPI_space = pe.Node(
interface=afni.Volreg(
outputtype='NIFTI_GZ',
zpad=5,
args=' -cubic ' # -twopass -Fourier
),
name='motion_correct_EPI_space')
motion_correct_all = pe.MapNode(
interface=afni.Volreg(
outputtype='NIFTI_GZ',
zpad=5,
args=' -cubic ' # -twopass
),
name='motion_correct_all',
iterfield=['in_file'])
# for renaming *_volreg.nii.gz to *_mcf.nii.gz
set_postfix_mcf = pe.MapNode(interface=Set_postfix,
name='set_postfix_mcf',
iterfield=['in_file'])
set_postfix_mcf.inputs.postfix = 'mcf'
rename_volreg = pe.MapNode(interface=Rename(keep_ext=True),
name='rename_volreg',
iterfield=['in_file', 'format_string'])
# curate for moco between sessions
motion_correction_workflow.connect(EPI_file_selector_node, 'out_file',
motion_correct_EPI_space, 'in_file')
motion_correction_workflow.connect(motion_correct_EPI_space,
'out_file', mean_bold, 'in_file')
# motion correction across runs
motion_correction_workflow.connect(input_node, 'in_files',
motion_correct_all, 'in_file')
motion_correction_workflow.connect(mean_bold, 'out_file',
motion_correct_all, 'basefile')
# motion_correction_workflow.connect(mean_bold, 'out_file', motion_correct_all, 'rotparent')
# motion_correction_workflow.connect(mean_bold, 'out_file', motion_correct_all, 'gridparent')
# output node:
motion_correction_workflow.connect(mean_bold, 'out_file', output_node,
'EPI_space_file')
motion_correction_workflow.connect(motion_correct_all, 'md1d_file',
output_node,
'max_displacement_info')
motion_correction_workflow.connect(motion_correct_all, 'oned_file',
output_node,
'motion_correction_parameter_info')
motion_correction_workflow.connect(
motion_correct_all, 'oned_matrix_save', output_node,
'motion_correction_parameter_matrix')
motion_correction_workflow.connect(input_node, 'in_files',
set_postfix_mcf, 'in_file')
motion_correction_workflow.connect(set_postfix_mcf, 'out_file',
rename_volreg, 'format_string')
motion_correction_workflow.connect(motion_correct_all, 'out_file',
rename_volreg, 'in_file')
motion_correction_workflow.connect(rename_volreg, 'out_file',
output_node,
'motion_corrected_files')
# datasink:
motion_correction_workflow.connect(mean_bold, 'out_file',
rename_mean_bold, 'in_file')
motion_correction_workflow.connect(rename_mean_bold, 'out_file',
datasink, 'reg')
motion_correction_workflow.connect(rename_volreg, 'out_file', datasink,
'mcf')
motion_correction_workflow.connect(motion_correct_all, 'md1d_file',
datasink,
'mcf.max_displacement_info')
motion_correction_workflow.connect(motion_correct_all, 'oned_file',
datasink, 'mcf.parameter_info')
motion_correction_workflow.connect(motion_correct_all,
'oned_matrix_save', datasink,
'mcf.motion_pars')
return motion_correction_workflow
def min_func_preproc(subject, sessions, data_dir, fs_dir, wd, sink, TR,
EPI_resolution):
#initiate min func preproc workflow
wf = pe.Workflow(name='MPP')
wf.base_dir = wd
wf.config['execution']['crashdump_dir'] = wf.base_dir + "/crash_files"
## set fsl output type to nii.gz
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# I/O nodes
inputnode = pe.Node(util.IdentityInterface(fields=['subjid', 'fs_dir']),
name='inputnode')
inputnode.inputs.subjid = subject
inputnode.inputs.fs_dir = fs_dir
ds = pe.Node(nio.DataSink(base_directory=sink, parameterization=False),
name='sink')
ds.inputs.substitutions = [('moco.nii.gz.par', 'moco.par'),
('moco.nii.gz_', 'moco_')]
#infosource to interate over sessions: COND, EXT1, EXT2
sessions_infosource = pe.Node(util.IdentityInterface(fields=['session']),
name='session')
sessions_infosource.iterables = [('session', sessions)]
#select files
templates = {
'func_data': '{session}/func_data.nii.gz',
'T1_brain': 'T1/T1_brain.nii.gz',
'wmedge': 'T1/MASKS/aparc_aseg.WMedge.nii.gz'
}
selectfiles = pe.Node(nio.SelectFiles(templates, base_directory=data_dir),
name='selectfiles')
wf.connect(sessions_infosource, 'session', selectfiles, 'session')
wf.connect(sessions_infosource, 'session', ds, 'container')
##########################################################################
######################## START ######################################
##########################################################################
###########################################################################
######################## No. 3 ######################################
#change the data type to float
fsl_float = pe.Node(fsl.maths.MathsCommand(output_datatype='float'),
name='fsl_float')
wf.connect(selectfiles, 'func_data', fsl_float, 'in_file')
###########################################################################
######################## No. 4 ######################################
#get FD from fsl_motion_outliers
FD = pe.Node(fsl.MotionOutliers(out_file='func_data_FD_outliers.txt',
out_metric_values='func_data_FD.txt',
metric='fd'),
name='FD')
wf.connect(fsl_float, 'out_file', FD, 'in_file')
wf.connect(FD, 'out_metric_values', ds, 'QC.@FD')
wf.connect(FD, 'out_file', ds, 'QC.@FDoutliers')
###########################################################################
######################## No. 5 ######################################
#slice timing correction: sequential ascending
slicetimer = pe.Node(
fsl.SliceTimer(
index_dir=False,
interleaved=False,
#slice_direction=3, #z direction
time_repetition=TR,
out_file='func_data_stc.nii.gz'),
name='slicetimer')
wf.connect(fsl_float, 'out_file', slicetimer, 'in_file')
wf.connect(slicetimer, 'slice_time_corrected_file', ds, 'TEMP.@slicetimer')
###########################################################################
######################## No. 6 ######################################
#do realignment to the middle or first volume
mcflirt = pe.Node(fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
ref_vol=1,
out_file='func_data_stc_moco.nii.gz'),
name='mcflirt')
wf.connect(slicetimer, 'slice_time_corrected_file', mcflirt, 'in_file')
wf.connect(mcflirt, 'out_file', ds, 'TEMP.@mcflirt')
wf.connect(mcflirt, 'par_file', ds, 'MOCO.@par_file')
wf.connect(mcflirt, 'rms_files', ds, 'MOCO.@rms_files')
wf.connect(mcflirt, 'mat_file', ds, 'MOCO_MAT.@mcflirt')
# plot motion parameters
rotplotter = pe.Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='rotations',
out_file='rotation.png'),
name='rotplotter')
transplotter = pe.Node(fsl.PlotMotionParams(in_source='fsl',
plot_type='translations',
out_file='translation.png'),
name='transplotter')
dispplotter = pe.Node(
interface=fsl.PlotMotionParams(in_source='fsl',
plot_type='displacement',
out_file='displacement.png'),
name='dispplotter')
wf.connect(mcflirt, 'par_file', rotplotter, 'in_file')
wf.connect(mcflirt, 'par_file', transplotter, 'in_file')
wf.connect(mcflirt, 'rms_files', dispplotter, 'in_file')
wf.connect(rotplotter, 'out_file', ds, 'PLOTS.@rotplot')
wf.connect(transplotter, 'out_file', ds, 'PLOTS.@transplot')
wf.connect(dispplotter, 'out_file', ds, 'PLOTS.@disppplot')
#calculate tSNR and the mean
moco_Tmean = pe.Node(fsl.maths.MathsCommand(args='-Tmean',
out_file='moco_Tmean.nii.gz'),
name='moco_Tmean')
moco_Tstd = pe.Node(fsl.maths.MathsCommand(args='-Tstd',
out_file='moco_Tstd.nii.gz'),
name='moco_Tstd')
tSNR0 = pe.Node(fsl.maths.MultiImageMaths(op_string='-div %s',
out_file='moco_tSNR.nii.gz'),
name='moco_tSNR')
wf.connect(mcflirt, 'out_file', moco_Tmean, 'in_file')
wf.connect(mcflirt, 'out_file', moco_Tstd, 'in_file')
wf.connect(moco_Tmean, 'out_file', tSNR0, 'in_file')
wf.connect(moco_Tstd, 'out_file', tSNR0, 'operand_files')
wf.connect(moco_Tmean, 'out_file', ds, 'TEMP.@moco_Tmean')
wf.connect(moco_Tstd, 'out_file', ds, 'TEMP.@moco_Tstd')
wf.connect(tSNR0, 'out_file', ds, 'TEMP.@moco_Tsnr')
###########################################################################
######################## No. 7 ######################################
#bias field correction of mean epi for better coregistration
bias = pe.Node(
fsl.FAST(
img_type=2,
#restored_image='epi_Tmeanrestored.nii.gz',
output_biascorrected=True,
out_basename='moco_Tmean',
no_pve=True,
probability_maps=False),
name='bias')
wf.connect(moco_Tmean, 'out_file', bias, 'in_files')
wf.connect(bias, 'restored_image', ds, 'TEMP.@restored_image')
#co-registration to anat using FS BBregister and mean EPI
bbregister = pe.Node(fs.BBRegister(
subject_id=subject,
subjects_dir=fs_dir,
contrast_type='t2',
init='fsl',
out_fsl_file='func2anat.mat',
out_reg_file='func2anat.dat',
registered_file='moco_Tmean_restored2anat.nii.gz',
epi_mask=True),
name='bbregister')
wf.connect(bias, 'restored_image', bbregister, 'source_file')
wf.connect(bbregister, 'registered_file', ds, 'TEMP.@registered_file')
wf.connect(bbregister, 'out_fsl_file', ds, 'COREG.@out_fsl_file')
wf.connect(bbregister, 'out_reg_file', ds, 'COREG.@out_reg_file')
wf.connect(bbregister, 'min_cost_file', ds, 'COREG.@min_cost_file')
#inverse func2anat mat
inverseXFM = pe.Node(fsl.ConvertXFM(invert_xfm=True,
out_file='anat2func.mat'),
name='inverseXFM')
wf.connect(bbregister, 'out_fsl_file', inverseXFM, 'in_file')
wf.connect(inverseXFM, 'out_file', ds, 'COREG.@out_fsl_file_inv')
#plot the corregistration quality
slicer = pe.Node(fsl.Slicer(middle_slices=True, out_file='func2anat.png'),
name='slicer')
wf.connect(selectfiles, 'wmedge', slicer, 'image_edges')
wf.connect(bbregister, 'registered_file', slicer, 'in_file')
wf.connect(slicer, 'out_file', ds, 'PLOTS.@func2anat')
###########################################################################
######################## No. 8 ######################################
#MOCO and COREGISTRATION
#resample T1 to EPI resolution to use it as a reference image
resample_T1 = pe.Node(
fsl.FLIRT(datatype='float',
apply_isoxfm=EPI_resolution,
out_file='T1_brain_EPI.nii.gz'),
#interp='nearestneighbour'),keep spline so it looks nicer
name='resample_T1')
wf.connect(selectfiles, 'T1_brain', resample_T1, 'in_file')
wf.connect(selectfiles, 'T1_brain', resample_T1, 'reference')
wf.connect(resample_T1, 'out_file', ds, 'COREG.@resample_T1')
#concate matrices (moco and func2anat) volume-wise
concat_xfm = pe.MapNode(fsl.ConvertXFM(concat_xfm=True),
iterfield=['in_file'],
name='concat_xfm')
wf.connect(mcflirt, 'mat_file', concat_xfm, 'in_file')
wf.connect(bbregister, 'out_fsl_file', concat_xfm, 'in_file2')
wf.connect(concat_xfm, 'out_file', ds, 'MOCO2ANAT_MAT.@concat_out')
#split func_data
split = pe.Node(fsl.Split(dimension='t'), name='split')
wf.connect(slicetimer, 'slice_time_corrected_file', split, 'in_file')
#motion correction and corregistration in one interpolation step
flirt = pe.MapNode(fsl.FLIRT(apply_xfm=True,
interp='spline',
datatype='float'),
iterfield=['in_file', 'in_matrix_file'],
name='flirt')
wf.connect(split, 'out_files', flirt, 'in_file')
wf.connect(resample_T1, 'out_file', flirt, 'reference')
wf.connect(concat_xfm, 'out_file', flirt, 'in_matrix_file')
#merge the files to have 4d dataset motion corrected and co-registerd to T1
merge = pe.Node(fsl.Merge(dimension='t',
merged_file='func_data_stc_moco2anat.nii.gz'),
name='merge')
wf.connect(flirt, 'out_file', merge, 'in_files')
wf.connect(merge, 'merged_file', ds, 'TEMP.@merged')
###########################################################################
######################## No. 9 ######################################
#run BET on co-registered EPI in 1mm and get the mask
bet = pe.Node(fsl.BET(mask=True,
functional=True,
out_file='moco_Tmean_restored2anat_BET.nii.gz'),
name='bet')
wf.connect(bbregister, 'registered_file', bet, 'in_file')
wf.connect(bet, 'out_file', ds, 'TEMP.@func_data_example')
wf.connect(bet, 'mask_file', ds, 'TEMP.@func_data_mask')
#resample BET mask to EPI resolution
resample_mask = pe.Node(fsl.FLIRT(
datatype='int',
apply_isoxfm=EPI_resolution,
interp='nearestneighbour',
out_file='prefiltered_func_data_mask.nii.gz'),
name='resample_mask')
wf.connect(bet, 'mask_file', resample_mask, 'in_file')
wf.connect(resample_T1, 'out_file', resample_mask, 'reference')
wf.connect(resample_mask, 'out_file', ds, '@mask')
#apply the mask to 4D data to get rid of the "eyes and the rest"
mask4D = pe.Node(fsl.maths.ApplyMask(), name='mask')
wf.connect(merge, 'merged_file', mask4D, 'in_file')
wf.connect(resample_mask, 'out_file', mask4D, 'mask_file')
###########################################################################
######################## No. 10 ######################################
#get the values necessary for intensity normalization
median = pe.Node(fsl.utils.ImageStats(op_string='-k %s -p 50'),
name='median')
wf.connect(resample_mask, 'out_file', median, 'mask_file')
wf.connect(mask4D, 'out_file', median, 'in_file')
#compute the scaling factor
def get_factor(val):
factor = 10000 / val
return factor
get_scaling_factor = pe.Node(util.Function(input_names=['val'],
output_names=['out_val'],
function=get_factor),
name='scaling_factor')
#normalize the 4D func data with one scaling factor
multiplication = pe.Node(fsl.maths.BinaryMaths(
operation='mul', out_file='prefiltered_func_data.nii.gz'),
name='multiplication')
wf.connect(median, 'out_stat', get_scaling_factor, 'val')
wf.connect(get_scaling_factor, 'out_val', multiplication, 'operand_value')
wf.connect(mask4D, 'out_file', multiplication, 'in_file')
wf.connect(multiplication, 'out_file', ds, '@prefiltered_func_data')
###########################################################################
######################## No. 11 ######################################
#calculate tSNR and the mean of the new prefiltered and detrend dataset
tsnr_detrend = pe.Node(misc.TSNR(
regress_poly=1,
detrended_file='prefiltered_func_data_detrend.nii.gz',
mean_file='prefiltered_func_data_detrend_Tmean.nii.gz',
tsnr_file='prefiltered_func_data_detrend_tSNR.nii.gz'),
name='tsnr_detrend')
wf.connect(multiplication, 'out_file', tsnr_detrend, 'in_file')
wf.connect(tsnr_detrend, 'tsnr_file', ds, 'QC.@tsnr_detrend')
wf.connect(tsnr_detrend, 'mean_file', ds, 'QC.@detrend_mean_file')
wf.connect(tsnr_detrend, 'detrended_file', ds, '@detrend_file')
#resample the EPI mask to original EPI dimensions
convert2func = pe.Node(fsl.FLIRT(apply_xfm=True,
interp='nearestneighbour',
out_file='func_data_mask2func.nii.gz'),
name='conver2func')
wf.connect(resample_mask, 'out_file', convert2func, 'in_file')
wf.connect(bias, 'restored_image', convert2func, 'reference')
wf.connect(inverseXFM, 'out_file', convert2func, 'in_matrix_file')
wf.connect(convert2func, 'out_file', ds, 'QC.@inv')
###########################################################################
######################## RUN ######################################
wf.write_graph(dotfilename='wf.dot',
graph2use='colored',
format='pdf',
simple_form=True)
wf.run(plugin='MultiProc', plugin_args={'n_procs': 2})
#wf.run()
return
def create_preprocess_mag_wf():
preprocmag = pe.Workflow(name="preprocmag")
preprocmag.config['execution']['remove_unnecessary_outputs'] = False
# define inputs
inputspec = pe.Node(ul.IdentityInterface(fields=['input_mag', # raw phase data
'frac', # BET franction (-f parameter)
'rest', # volumes of rest in block design
'task', # volumes of task in block design
]),
name='inputspec')
# convert image to float
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float', op_string='', suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
# motion correct each run
volreg = pe.MapNode(interface=afni.Volreg(), name='volreg', iterfield='in_file')
volreg.inputs.outputtype = 'NIFTI_GZ'
# calculate relative motions
calcrel = pe.MapNode(ul.Function(['in_file'], ['out_file'], calcrelmotion),
name='calcrel', iterfield=['in_file'])
#generate motion plots
plotmc = pe.MapNode(interface=fsl.PlotMotionParams(), name='plotmc', iterfield='in_file')
plotmc.inputs.in_source = 'fsl'
plotmc.iterables = ("plot_type", ['rotations', 'translations', 'displacement'])
# register each run to first volume of first run
# A) extract the first volume of the first run
extract_ref = pe.MapNode(interface=fsl.ExtractROI(t_size=1, t_min=0), name='extract_ref', iterfield=['in_file'])
# B) registration
align2first = pe.MapNode(interface=afni.Allineate(), name='align2first', iterfield=['in_file'])
align2first.inputs.num_threads = 2
align2first.inputs.out_matrix = 'align2first'
# merge xfm from moco and first run alignment
merge_xfm = pe.MapNode(interface=ul.Merge(2), name='merge_xfm', iterfield=['in1', 'in2'])
# concatenate moco and alignment to run 1
cat_xfm = pe.MapNode(interface=afni.CatMatvec(oneline=True), name='cat_xfm', iterfield=['in_file'])
cat_xfm.inputs.out_file = 'concated_xfm.aff12.1D'
# apply first volume registration and motion correction in a single step
applyalign = pe.MapNode(interface=afni.Allineate(), name='applyalign', iterfield=['in_file', 'in_matrix'])
applyalign.inputs.num_threads = 2
applyalign.inputs.final_interpolation = 'nearestneighbour'
applyalign.inputs.outputtype = 'NIFTI_GZ'
# afni messes with the header (unobliques the data) this puts it back
cpgeommoco = pe.MapNode(interface=fsl.CopyGeom(), name='cpgeommoco', iterfield=['dest_file', 'in_file'])
# linear detrending prior to SNR calculation
detrend = pe.MapNode(interface=pp.DetrendMag(), name='detrend', iterfield=['mag'])
# get the mean functional of run 1 for brain extraction
meanfunc = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
name='meanfunc', iterfield=['in_file'])
# calculate the phase noise (takes in volume of activation, if none provided them assumes resting state)
calcSNR = pe.MapNode(interface=pp.RestAverage(), name='calcSNR', iterfield=['func', 'rest', 'task'])
# extract brain with fsl and save the mask
extractor = pe.Node(interface=fsl.BET(), name="extractor")
extractor.inputs.mask = True
# apply the mask to all runs
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file'],
name='maskfunc')
# outputspec
outputspec = pe.Node(ul.IdentityInterface(fields=['proc_mag','motion_par',
'motion_data', 'maxdisp_data' ,
'motion_plot', 'run_txfm',
'mask_file','mean_file','snr']),
name='outputspec')
preprocmag = pe.Workflow(name='preprocmag')
preprocmag.connect([(inputspec, img2float, [('input_mag', 'in_file')]),
(img2float, volreg, [('out_file', 'in_file')]),
(volreg, extract_ref, [('out_file', 'in_file')]),
(extract_ref, align2first, [('roi_file', 'in_file')]),
(extract_ref, align2first, [(('roi_file', pickfirst), 'reference')]),
(extract_ref, applyalign, [(('roi_file', pickfirst), 'reference')]),
(volreg, merge_xfm, [('oned_matrix_save', 'in2')]),
(align2first, merge_xfm, [('out_matrix', 'in1')]),
(merge_xfm, cat_xfm, [(('out', wraptuple), 'in_file')]),
(volreg,applyalign, [('out_file', 'in_file')]),
(volreg, calcrel, [('md1d_file', 'in_file')]),
(volreg, plotmc, [('oned_file', 'in_file')]),
(cat_xfm, applyalign, [('out_file', 'in_matrix')]),
(img2float, cpgeommoco, [('out_file', 'in_file')]),
(applyalign, cpgeommoco, [('out_file', 'dest_file')]),
(cpgeommoco, detrend, [('out_file', 'mag')]),
(detrend, meanfunc, [('detrended_mag', 'in_file')]),
(inputspec, calcSNR, [('rest', 'rest'),
('task', 'task')]),
(detrend, calcSNR, [('detrended_mag', 'func')]),
(inputspec, extractor, [('frac', 'frac')]),
(meanfunc, extractor, [(('out_file', pickfirst), 'in_file')]),
(cpgeommoco, maskfunc, [('out_file', 'in_file')]),
(extractor, maskfunc, [('mask_file', 'in_file2')]),
(maskfunc, outputspec, [('out_file', 'proc_mag')]),
(volreg, outputspec, [('oned_matrix_save', 'motion_par')]),
(volreg, outputspec, [('oned_file', 'motion_data')]),
(volreg, outputspec, [('md1d_file', 'maxdisp_data')]),
(plotmc, outputspec, [('out_file', 'motion_plot')]),
(cat_xfm, outputspec, [('out_file', 'run_txfm')]),
(extractor, outputspec, [('mask_file', 'mask_file')]),
(extractor, outputspec, [('out_file', 'mean_file')]),
(calcSNR, outputspec, [('tsnr', 'snr')]),
])
return preprocmag
def __motion_correct_file__(
self,
input_file,
output_file,
subject,
directory,
use_example_pp=False):
# Check whether motion correction has already been completed
print ">>>> Working on {}".format(input_file)
if use_example_pp:
pp.preproc.inputs.inputspec.func = input_file
pp.preproc.inputs.inputspec.struct = os.path.join(
subject.anatomical_dir(), 'highres001.nii.gz')
pp.preproc.base_dir = directory
pp.preproc.run()
# TODO: copy motion correction photos as well
intnorm_file = output_file.replace('.nii.gz', '_intnorm.nii.gz')
shutil.copy(
os.path.join(
directory,
'preproc',
'intnorm',
'mapflow',
'_intnorm0',
'bold_dtype_mcf_mask_intnorm.nii.gz'),
intnorm_file)
shutil.copy(
os.path.join(
directory,
'preproc',
'maskfunc2',
'mapflow',
'_maskfunc20',
'bold_dtype_mcf_mask.nii.gz'),
output_file)
cmd = "eog {}".format(
os.path.join(
directory,
'preproc',
'realign',
'mapflow',
'_realign0',
'bold_dtype_mcf.nii.gz_rot.png'))
subprocess.Popen(
cmd,
stdout=subprocess.PIPE,
shell=True,
preexec_fn=os.setsid)
cmd = "eog {}".format(
os.path.join(
directory,
'preproc',
'realign',
'mapflow',
'_realign0',
'bold_dtype_mcf.nii.gz_trans.png'))
subprocess.Popen(
cmd,
stdout=subprocess.PIPE,
shell=True,
preexec_fn=os.setsid)
else:
mcflt = fsl.MCFLIRT(
in_file=input_file,
out_file=output_file,
save_plots=True)
result = mcflt.run()
pmp = fsl.PlotMotionParams(
in_file=result.outputs.par_file, in_source='fsl')
pmp.inputs.plot_type = 'rotations'
pmp.run()
pmp.inputs.plot_type = 'translations'
pmp.run()
iterfield=['in_file', 'in_matrix_file', 'reference', 'wm_seg'])
NodeHash_a9682a0.inputs.cost = 'bbr'
NodeHash_a9682a0.inputs.dof = 6
NodeHash_a9682a0.inputs.no_resample = True
#Wraps command **mcflirt**
NodeHash_de46680 = pe.MapNode(interface=fsl.MCFLIRT(),
name='NodeName_de46680',
iterfield=['in_file', 'ref_file'])
NodeHash_de46680.inputs.interpolation = 'spline'
NodeHash_de46680.inputs.save_mats = True
NodeHash_de46680.inputs.save_plots = True
NodeHash_de46680.inputs.save_rms = True
#Wraps command **fsl_tsplot**
NodeHash_e827000 = pe.MapNode(interface=fsl.PlotMotionParams(),
name='NodeName_e827000',
iterfield=['in_file'])
NodeHash_e827000.inputs.args = '-a x,y,z -w 640 -h 144'
NodeHash_e827000.inputs.in_source = 'fsl'
NodeHash_e827000.iterables = [('plot_type', ['rotations', 'translations'])]
#Wraps command **fslmaths**
NodeHash_12ef2460 = pe.MapNode(interface=fsl.MeanImage(),
name='NodeName_12ef2460',
iterfield=['in_file'])
NodeHash_12ef2460.inputs.dimension = 'T'
#Wraps command **bet**
NodeHash_131f40e0 = pe.MapNode(interface=fsl.BET(),
name='NodeName_131f40e0',
def create_featreg_preproc(name='featpreproc',
whichvol='middle',
deletetimepoints=4):
"""Create a FEAT preprocessing workflow with registration to one volume of the first run
Parameters
----------
name : name of workflow (default: featpreproc)
whichvol : which volume of the first run to register to ('first', 'middle', 'mean')
Inputs::
inputspec.func : functional runs (filename or list of filenames)
inputspec.fwhm : fwhm for smoothing with SUSAN
inputspec.highpass : HWHM in TRs (if created with highpass=True)
Outputs::
outputspec.reference : volume to which runs are realigned
outputspec.motion_parameters : motion correction parameters
outputspec.realigned_files : motion corrected files
outputspec.motion_plots : plots of motion correction parameters
outputspec.mask : mask file used to mask the brain
outputspec.smoothed_files : smoothed functional data
outputspec.meanscaled_files : meanscaled data
Example
-------
>>> from nipype.workflows.fsl import create_featreg_preproc
>>> import os
>>> preproc = create_featreg_preproc()
>>> preproc.inputs.inputspec.func = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.fwhm = 5
>>> preproc.inputs.inputspec.highpass = 128./(2*2.5)
>>> preproc.base_dir = '/tmp'
>>> preproc.run() # doctest: +SKIP
>>> preproc = create_featreg_preproc(highpass=False, whichvol='mean')
>>> preproc.inputs.inputspec.func = 'f3.nii'
>>> preproc.inputs.inputspec.fwhm = 5
>>> preproc.base_dir = '/tmp'
>>> preproc.run() # doctest: +SKIP
"""
featpreproc = pe.Workflow(name=name)
# Set up a node to define all inputs and outputs required for the
# preprocessing workflow
inputnode = pe.Node(interface=util.IdentityInterface(fields=[
'func',
'fwhm',
]),
name='inputspec')
outputnode = pe.Node(interface=util.IdentityInterface(fields=[
'reference',
'motion_parameters',
'realigned_files',
'motion_rot_plots',
'motion_trans_plots',
'mask',
'maskfunc_files',
'smoothed_files',
'meanscaled_files',
]),
name='outputspec')
# Convert functional images to float representation. Since there can
# be more than one functional run we use a MapNode to convert each
# run.
deletevol = pe.MapNode(interface=fsl.ExtractROI(t_min=deletetimepoints),
iterfield=['in_file', 't_size'],
name='deletevol')
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
featpreproc.connect(inputnode, 'func', deletevol, 'in_file')
featpreproc.connect(inputnode, ('func', getTTP, deletetimepoints),
deletevol, 't_size')
featpreproc.connect(deletevol, 'roi_file', img2float, 'in_file')
# Extract the first volume of the each run as the reference
if whichvol != 'mean':
extract_ref = pe.MapNode(interface=fsl.ExtractROI(t_size=1),
iterfield=['in_file'],
name='extractref')
featpreproc.connect(img2float, 'out_file', extract_ref, 'in_file')
featpreproc.connect(img2float, ('out_file', pickvol, 0, whichvol),
extract_ref, 't_min')
featpreproc.connect(extract_ref, 'roi_file', outputnode, 'reference')
# Realign the functional runs to the reference (1st volume of first run)
motion_correct = pe.MapNode(interface=fsl.MCFLIRT(save_mats=True,
save_plots=True,
save_rms=True,
interpolation='sinc'),
name='realign',
iterfield=['in_file', 'ref_file'])
featpreproc.connect(img2float, 'out_file', motion_correct, 'in_file')
if whichvol != 'mean':
featpreproc.connect(extract_ref, 'roi_file', motion_correct,
'ref_file')
else:
motion_correct.inputs.mean_vol = True
featpreproc.connect(motion_correct, 'mean_img', outputnode,
'reference')
featpreproc.connect(motion_correct, 'par_file', outputnode,
'motion_parameters')
featpreproc.connect(motion_correct, 'out_file', outputnode,
'realigned_files')
# Plot the estimated motion parameters
plot_rotations = pe.MapNode(interface=fsl.PlotMotionParams(
in_source='fsl', plot_type='rotations'),
name='plot_rotations',
iterfield=['in_file'])
plot_translations = pe.MapNode(interface=fsl.PlotMotionParams(
in_source='fsl', plot_type='translations'),
name='plot_translations',
iterfield=['in_file'])
# plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
featpreproc.connect(motion_correct, 'par_file', plot_rotations, 'in_file')
featpreproc.connect(motion_correct, 'par_file', plot_translations,
'in_file')
featpreproc.connect(plot_rotations, 'out_file', outputnode,
'motion_rot_plots')
featpreproc.connect(plot_translations, 'out_file', outputnode,
'motion_trans_plots')
# Extract the mean volume of the first functional run
meanfunc = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc')
featpreproc.connect(motion_correct, 'out_file', meanfunc, 'in_file')
# Strip the skull from the mean functional to generate a mask
meanfuncmask = pe.MapNode(interface=fsl.BET(mask=True,
no_output=True,
frac=0.3),
iterfield=['in_file'],
name='meanfuncmask')
featpreproc.connect(meanfunc, 'out_file', meanfuncmask, 'in_file')
# Mask the functional runs with the extracted mask
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc')
featpreproc.connect(motion_correct, 'out_file', maskfunc, 'in_file')
featpreproc.connect(meanfuncmask, 'mask_file', maskfunc, 'in_file2')
# Determine the 2nd and 98th percentile intensities of each functional run
getthresh = pe.MapNode(interface=fsl.ImageStats(op_string='-p 2 -p 98'),
iterfield=['in_file'],
name='getthreshold')
featpreproc.connect(maskfunc, 'out_file', getthresh, 'in_file')
# Threshold the first run of the functional data at 10% of the 98th percentile
threshold = pe.MapNode(interface=fsl.ImageMaths(out_data_type='char',
suffix='_thresh'),
iterfield=['in_file', 'op_string'],
name='threshold')
featpreproc.connect(maskfunc, 'out_file', threshold, 'in_file')
# Define a function to get 10% of the intensity
featpreproc.connect(getthresh, ('out_stat', getthreshop), threshold,
'op_string')
# Determine the median value of the functional runs using the mask
medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
iterfield=['in_file', 'mask_file'],
name='medianval')
featpreproc.connect(motion_correct, 'out_file', medianval, 'in_file')
featpreproc.connect(threshold, 'out_file', medianval, 'mask_file')
# Dilate the mask
dilatemask = pe.MapNode(interface=fsl.ImageMaths(suffix='_dil',
op_string='-dilF'),
iterfield=['in_file'],
name='dilatemask')
featpreproc.connect(threshold, 'out_file', dilatemask, 'in_file')
featpreproc.connect(dilatemask, 'out_file', outputnode, 'mask')
# Mask the motion corrected functional runs with the dilated mask
maskfunc2 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc2')
featpreproc.connect(motion_correct, 'out_file', maskfunc2, 'in_file')
featpreproc.connect(dilatemask, 'out_file', maskfunc2, 'in_file2')
featpreproc.connect(maskfunc2, 'out_file', outputnode, 'maskfunc_files')
# Smooth each run using SUSAN with the brightness threshold set to 75%
# of the median value for each run and a mask consituting the mean
# functional
smooth = create_susan_smooth()
featpreproc.connect(inputnode, 'fwhm', smooth, 'inputnode.fwhm')
featpreproc.connect(maskfunc2, 'out_file', smooth, 'inputnode.in_files')
featpreproc.connect(dilatemask, 'out_file', smooth, 'inputnode.mask_file')
# Mask the smoothed data with the dilated mask
maskfunc3 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc3')
featpreproc.connect(smooth, 'outputnode.smoothed_files', maskfunc3,
'in_file')
featpreproc.connect(dilatemask, 'out_file', maskfunc3, 'in_file2')
concatnode = pe.Node(interface=util.Merge(2), name='concat')
featpreproc.connect(maskfunc2, ('out_file', tolist), concatnode, 'in1')
featpreproc.connect(maskfunc3, ('out_file', tolist), concatnode, 'in2')
# The following nodes select 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.
selectnode = pe.Node(interface=util.Select(), name='select')
featpreproc.connect(concatnode, 'out', selectnode, 'inlist')
featpreproc.connect(inputnode, ('fwhm', chooseindex), selectnode, 'index')
featpreproc.connect(selectnode, 'out', outputnode, 'smoothed_files')
# Scale the median value of the run is set to 10000
meanscale = pe.MapNode(interface=fsl.ImageMaths(suffix='_gms'),
iterfield=['in_file', 'op_string'],
name='meanscale')
featpreproc.connect(selectnode, 'out', meanscale, 'in_file')
featpreproc.connect(medianval, ('out_stat', getmeanscale), meanscale,
'op_string')
# Mask the scaled data with the dilated mask
maskfunc4 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc4')
featpreproc.connect(meanscale, 'out_file', maskfunc4, 'in_file')
featpreproc.connect(dilatemask, 'out_file', maskfunc4, 'in_file2')
featpreproc.connect(maskfunc4, 'out_file', outputnode, 'meanscaled_files')
return featpreproc
def create_featreg_preproc(name='featpreproc',
highpass=True,
whichvol='middle',
whichrun=0):
"""Create a FEAT preprocessing workflow with registration to one volume of
the first run. If whichvol = None and/or whichrun = None, no motion
correction will be performed and the FEAT preprocessing workflow will not
return outputspec.reference, outputspec.realigned_files, and
outputspec.motion_plots.
Parameters
----------
::
name : name of workflow (default: featpreproc)
highpass : boolean (default: True)
whichvol : which volume of the first run to register to ('first', 'middle', 'last', 'mean', None)
whichrun : which run to draw reference volume from (integer index or 'first', 'middle', 'last' or None)
Inputs::
inputspec.func : functional runs (filename or list of filenames)
inputspec.fwhm : fwhm for smoothing with SUSAN
inputspec.highpass : HWHM in TRs (if created with highpass=True)
Outputs::
outputspec.reference : volume to which runs are realigned
outputspec.motion_parameters : motion correction parameters
outputspec.realigned_files : motion corrected files
outputspec.motion_plots : plots of motion correction parameters
outputspec.mask : mask file used to mask the brain
outputspec.smoothed_files : smoothed functional data
outputspec.highpassed_files : highpassed functional data (if highpass=True)
outputspec.mean : mean file
Example
-------
>>> preproc = create_featreg_preproc()
>>> preproc.inputs.inputspec.func = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.fwhm = 5
>>> preproc.inputs.inputspec.highpass = 128./(2*2.5)
>>> preproc.base_dir = '/tmp'
>>> preproc.run() # doctest: +SKIP
>>> preproc = create_featreg_preproc(highpass=False, whichvol='mean')
>>> preproc.inputs.inputspec.func = 'f3.nii'
>>> preproc.inputs.inputspec.fwhm = 5
>>> preproc.base_dir = '/tmp'
>>> preproc.run() # doctest: +SKIP
"""
version = 0
if fsl.Info.version() and \
LooseVersion(fsl.Info.version()) > LooseVersion('5.0.6'):
version = 507
featpreproc = pe.Workflow(name=name)
"""
Derive boolean motion correction parameter from the given parameters
"""
if (whichrun != None) & (whichvol != None):
motion_corr = True
else:
motion_corr = False
"""
Set up a node to define all inputs required for the preprocessing workflow
"""
output_fields = ['mask', 'smoothed_files', 'mean', 'functional_files']
input_fields = ['func', 'fwhm']
if highpass:
output_fields += ['highpassed_files']
input_fields += ['highpass']
inputnode = pe.Node(
interface=util.IdentityInterface(fields=input_fields),
name='inputspec')
if motion_corr:
output_fields += [
'reference', 'motion_parameters', 'realigned_files'
]
outputnode = pe.Node(
interface=util.IdentityInterface(fields=output_fields),
name='outputspec')
else:
outputnode = pe.Node(
interface=util.IdentityInterface(fields=output_fields),
name='outputspec')
else:
inputnode = pe.Node(
interface=util.IdentityInterface(fields=input_fields),
name='inputspec')
if motion_corr:
output_fields += [
'reference', 'motion_parameters', 'realigned_files'
]
outputnode = pe.Node(
interface=util.IdentityInterface(fields=output_fields),
name='outputspec')
"""
Set up a node to define outputs for the preprocessing workflow
"""
"""
Convert functional images to float representation. Since there can
be more than one functional run we use a MapNode to convert each
run.
"""
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string='',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
featpreproc.connect(inputnode, 'func', img2float, 'in_file')
if motion_corr:
"""
Extract the middle (or what whichvol points to) volume of the first run as the reference
"""
if whichvol != 'mean':
extract_ref = pe.Node(interface=fsl.ExtractROI(t_size=1),
iterfield=['in_file'],
name='extractref')
featpreproc.connect(img2float, ('out_file', pickrun, whichrun),
extract_ref, 'in_file')
featpreproc.connect(img2float, ('out_file', pickvol, 0, whichvol),
extract_ref, 't_min')
featpreproc.connect(extract_ref, 'roi_file', outputnode,
'reference')
"""
Realign the functional runs to the reference (`whichvol` volume of first run)
"""
motion_correct = pe.MapNode(interface=fsl.MCFLIRT(
save_mats=True, save_plots=True, interpolation='spline'),
name='realign',
iterfield=['in_file'])
featpreproc.connect(img2float, 'out_file', motion_correct, 'in_file')
if whichvol != 'mean':
featpreproc.connect(extract_ref, 'roi_file', motion_correct,
'ref_file')
else:
motion_correct.inputs.mean_vol = True
featpreproc.connect(motion_correct,
('mean_img', pickrun, whichrun), outputnode,
'reference')
featpreproc.connect(motion_correct, 'par_file', outputnode,
'motion_parameters')
featpreproc.connect(motion_correct, 'out_file', outputnode,
'realigned_files')
"""
Plot the estimated motion parameters
"""
plot_motion = pe.MapNode(
interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
featpreproc.connect(motion_correct, 'par_file', plot_motion, 'in_file')
featpreproc.connect(plot_motion, 'out_file', outputnode,
'motion_plots')
"""
Extract the mean volume of the first functional run
"""
else:
featpreproc.connect(img2float, 'out_file', outputnode,
'functional_files')
#TODO: check whether this is really necessary
if motion_corr:
meanfunc = pe.Node(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
name='meanfunc')
featpreproc.connect(motion_correct, ('out_file', pickrun, whichrun),
meanfunc, 'in_file')
else:
meanfunc = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc')
featpreproc.connect(img2float, 'out_file', meanfunc, 'in_file')
"""
Strip the skull from the mean functional to generate a mask
"""
if motion_corr:
meanfuncmask = pe.Node(interface=fsl.BET(mask=True,
no_output=True,
frac=0.3),
name='meanfuncmask')
else:
meanfuncmask = pe.MapNode(interface=fsl.BET(mask=True,
no_output=True,
frac=0.3),
iterfield=['in_file'],
name='meanfuncmask')
featpreproc.connect(meanfunc, 'out_file', meanfuncmask, 'in_file')
"""
Mask the functional runs with the extracted mask
"""
if motion_corr:
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file'],
name='maskfunc')
featpreproc.connect(motion_correct, 'out_file', maskfunc, 'in_file')
else:
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc')
featpreproc.connect(img2float, 'out_file', maskfunc, 'in_file')
featpreproc.connect(meanfuncmask, 'mask_file', maskfunc, 'in_file2')
"""
Determine the 2nd and 98th percentile intensities of each functional run
"""
getthresh = pe.MapNode(interface=fsl.ImageStats(op_string='-p 2 -p 98'),
iterfield=['in_file'],
name='getthreshold')
featpreproc.connect(maskfunc, 'out_file', getthresh, 'in_file')
"""
Threshold the first run of the functional data at 10% of the 98th percentile
"""
threshold = pe.MapNode(interface=fsl.ImageMaths(out_data_type='char',
suffix='_thresh'),
iterfield=['in_file', 'op_string'],
name='threshold')
featpreproc.connect(maskfunc, 'out_file', threshold, 'in_file')
"""
Define a function to get 10% of the intensity
"""
featpreproc.connect(getthresh, ('out_stat', getthreshop), threshold,
'op_string')
"""
Determine the median value of the functional runs using the mask
"""
medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
iterfield=['in_file', 'mask_file'],
name='medianval')
if motion_corr:
featpreproc.connect(motion_correct, 'out_file', medianval, 'in_file')
else:
featpreproc.connect(img2float, 'out_file', medianval, 'in_file')
featpreproc.connect(threshold, 'out_file', medianval, 'mask_file')
"""
Dilate the mask
"""
dilatemask = pe.MapNode(interface=fsl.ImageMaths(suffix='_dil',
op_string='-dilF'),
iterfield=['in_file'],
name='dilatemask')
featpreproc.connect(threshold, 'out_file', dilatemask, 'in_file')
featpreproc.connect(dilatemask, 'out_file', outputnode, 'mask')
"""
Mask the motion corrected functional runs with the dilated mask
"""
maskfunc2 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc2')
if motion_corr:
featpreproc.connect(motion_correct, 'out_file', maskfunc2, 'in_file')
else:
featpreproc.connect(img2float, 'out_file', maskfunc2, 'in_file')
featpreproc.connect(dilatemask, 'out_file', maskfunc2, 'in_file2')
"""
Smooth each run using SUSAN with the brightness threshold set to 75%
of the median value for each run and a mask constituting the mean
functional
"""
smooth = create_susan_smooth()
featpreproc.connect(inputnode, 'fwhm', smooth, 'inputnode.fwhm')
featpreproc.connect(maskfunc2, 'out_file', smooth, 'inputnode.in_files')
featpreproc.connect(dilatemask, 'out_file', smooth, 'inputnode.mask_file')
"""
Mask the smoothed data with the dilated mask
"""
maskfunc3 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc3')
featpreproc.connect(smooth, 'outputnode.smoothed_files', maskfunc3,
'in_file')
featpreproc.connect(dilatemask, 'out_file', maskfunc3, 'in_file2')
concatnode = pe.Node(interface=util.Merge(2), name='concat')
featpreproc.connect(maskfunc2, ('out_file', tolist), concatnode, 'in1')
featpreproc.connect(maskfunc3, ('out_file', tolist), concatnode, 'in2')
"""
The following nodes select 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.
"""
selectnode = pe.Node(interface=util.Select(), name='select')
featpreproc.connect(concatnode, 'out', selectnode, 'inlist')
featpreproc.connect(inputnode, ('fwhm', chooseindex), selectnode, 'index')
featpreproc.connect(selectnode, 'out', outputnode, 'smoothed_files')
"""
Scale the median value of the run is set to 10000
"""
meanscale = pe.MapNode(interface=fsl.ImageMaths(suffix='_gms'),
iterfield=['in_file', 'op_string'],
name='meanscale')
featpreproc.connect(selectnode, 'out', meanscale, 'in_file')
"""
Define a function to get the scaling factor for intensity normalization
"""
featpreproc.connect(medianval, ('out_stat', getmeanscale), meanscale,
'op_string')
"""
Generate a mean functional image from the first run
"""
meanfunc3 = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc3')
if motion_corr:
featpreproc.connect(meanscale, ('out_file', pickrun, whichrun),
meanfunc3, 'in_file')
else:
featpreproc.connect(meanscale, 'out_file', meanfunc3, 'in_file')
featpreproc.connect(meanfunc3, 'out_file', outputnode, 'mean')
"""
Perform temporal highpass filtering on the data
"""
if highpass:
highpass = pe.MapNode(interface=fsl.ImageMaths(suffix='_tempfilt'),
iterfield=['in_file'],
name='highpass')
featpreproc.connect(inputnode, ('highpass', highpass_operand),
highpass, 'op_string')
featpreproc.connect(meanscale, 'out_file', highpass, 'in_file')
if version < 507:
featpreproc.connect(highpass, 'out_file', outputnode,
'highpassed_files')
else:
"""
Add back the mean removed by the highpass filter operation as of FSL 5.0.7
"""
meanfunc4 = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc4')
featpreproc.connect(meanscale, 'out_file', meanfunc4, 'in_file')
addmean = pe.MapNode(interface=fsl.BinaryMaths(operation='add'),
iterfield=['in_file', 'operand_file'],
name='addmean')
featpreproc.connect(highpass, 'out_file', addmean, 'in_file')
featpreproc.connect(meanfunc4, 'out_file', addmean, 'operand_file')
featpreproc.connect(addmean, 'out_file', outputnode,
'highpassed_files')
return featpreproc
def create_parallelfeat_preproc(name='featpreproc', highpass=True):
"""Preprocess each run with FSL independently of the others
Parameters
----------
::
name : name of workflow (default: featpreproc)
highpass : boolean (default: True)
Inputs::
inputspec.func : functional runs (filename or list of filenames)
inputspec.fwhm : fwhm for smoothing with SUSAN
inputspec.highpass : HWHM in TRs (if created with highpass=True)
Outputs::
outputspec.reference : volume to which runs are realigned
outputspec.motion_parameters : motion correction parameters
outputspec.realigned_files : motion corrected files
outputspec.motion_plots : plots of motion correction parameters
outputspec.mask : mask file used to mask the brain
outputspec.smoothed_files : smoothed functional data
outputspec.highpassed_files : highpassed functional data (if highpass=True)
outputspec.mean : mean file
Example
-------
>>> preproc = create_parallelfeat_preproc()
>>> preproc.inputs.inputspec.func = ['f3.nii', 'f5.nii']
>>> preproc.inputs.inputspec.fwhm = 5
>>> preproc.inputs.inputspec.highpass = 128./(2*2.5)
>>> preproc.base_dir = '/tmp'
>>> preproc.run() # doctest: +SKIP
>>> preproc = create_parallelfeat_preproc(highpass=False)
>>> preproc.inputs.inputspec.func = 'f3.nii'
>>> preproc.inputs.inputspec.fwhm = 5
>>> preproc.base_dir = '/tmp'
>>> preproc.run() # doctest: +SKIP
"""
featpreproc = pe.Workflow(name=name)
"""
Set up a node to define all inputs required for the preprocessing workflow
"""
if highpass:
inputnode = pe.Node(interface=util.IdentityInterface(fields=['func',
'fwhm',
'highpass']),
name='inputspec')
outputnode = pe.Node(interface=util.IdentityInterface(fields=['reference',
'motion_parameters',
'realigned_files',
'motion_plots',
'mask',
'smoothed_files',
'highpassed_files',
'mean']),
name='outputspec')
else:
inputnode = pe.Node(interface=util.IdentityInterface(fields=['func',
'fwhm']),
name='inputspec')
outputnode = pe.Node(interface=util.IdentityInterface(fields=['reference',
'motion_parameters',
'realigned_files',
'motion_plots',
'mask',
'smoothed_files',
'mean']),
name='outputspec')
"""
Set up a node to define outputs for the preprocessing workflow
"""
"""
Convert functional images to float representation. Since there can
be more than one functional run we use a MapNode to convert each
run.
"""
img2float = pe.MapNode(interface=fsl.ImageMaths(out_data_type='float',
op_string = '',
suffix='_dtype'),
iterfield=['in_file'],
name='img2float')
featpreproc.connect(inputnode, 'func', img2float, 'in_file')
"""
Extract the first volume of the first run as the reference
"""
extract_ref = pe.MapNode(interface=fsl.ExtractROI(t_size=1),
iterfield=['in_file', 't_min'],
name = 'extractref')
featpreproc.connect(img2float, 'out_file', extract_ref, 'in_file')
featpreproc.connect(img2float, ('out_file', pickmiddle), extract_ref, 't_min')
featpreproc.connect(extract_ref, 'roi_file', outputnode, 'reference')
"""
Realign the functional runs to the reference (1st volume of first run)
"""
motion_correct = pe.MapNode(interface=fsl.MCFLIRT(save_mats = True,
save_plots = True),
name='realign',
iterfield = ['in_file', 'ref_file'])
featpreproc.connect(img2float, 'out_file', motion_correct, 'in_file')
featpreproc.connect(extract_ref, 'roi_file', motion_correct, 'ref_file')
featpreproc.connect(motion_correct, 'par_file', outputnode, 'motion_parameters')
featpreproc.connect(motion_correct, 'out_file', outputnode, 'realigned_files')
"""
Plot the estimated motion parameters
"""
plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
featpreproc.connect(motion_correct, 'par_file', plot_motion, 'in_file')
featpreproc.connect(plot_motion, 'out_file', outputnode, 'motion_plots')
"""
Extract the mean volume of the first functional run
"""
meanfunc = pe.MapNode(interface=fsl.ImageMaths(op_string = '-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc')
featpreproc.connect(motion_correct, 'out_file', meanfunc, 'in_file')
"""
Strip the skull from the mean functional to generate a mask
"""
meanfuncmask = pe.MapNode(interface=fsl.BET(mask = True,
no_output=True,
frac = 0.3),
iterfield=['in_file'],
name = 'meanfuncmask')
featpreproc.connect(meanfunc, 'out_file', meanfuncmask, 'in_file')
"""
Mask the functional runs with the extracted mask
"""
maskfunc = pe.MapNode(interface=fsl.ImageMaths(suffix='_bet',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name = 'maskfunc')
featpreproc.connect(motion_correct, 'out_file', maskfunc, 'in_file')
featpreproc.connect(meanfuncmask, 'mask_file', maskfunc, 'in_file2')
"""
Determine the 2nd and 98th percentile intensities of each functional run
"""
getthresh = pe.MapNode(interface=fsl.ImageStats(op_string='-p 2 -p 98'),
iterfield = ['in_file'],
name='getthreshold')
featpreproc.connect(maskfunc, 'out_file', getthresh, 'in_file')
"""
Threshold the first run of the functional data at 10% of the 98th percentile
"""
threshold = pe.MapNode(interface=fsl.ImageMaths(out_data_type='char',
suffix='_thresh'),
iterfield=['in_file', 'op_string'],
name='threshold')
featpreproc.connect(maskfunc, 'out_file', threshold, 'in_file')
"""
Define a function to get 10% of the intensity
"""
featpreproc.connect(getthresh, ('out_stat', getthreshop), threshold, 'op_string')
"""
Determine the median value of the functional runs using the mask
"""
medianval = pe.MapNode(interface=fsl.ImageStats(op_string='-k %s -p 50'),
iterfield = ['in_file', 'mask_file'],
name='medianval')
featpreproc.connect(motion_correct, 'out_file', medianval, 'in_file')
featpreproc.connect(threshold, 'out_file', medianval, 'mask_file')
"""
Dilate the mask
"""
dilatemask = pe.MapNode(interface=fsl.ImageMaths(suffix='_dil',
op_string='-dilF'),
iterfield=['in_file'],
name='dilatemask')
featpreproc.connect(threshold, 'out_file', dilatemask, 'in_file')
featpreproc.connect(dilatemask, 'out_file', outputnode, 'mask')
"""
Mask the motion corrected functional runs with the dilated mask
"""
maskfunc2 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc2')
featpreproc.connect(motion_correct, 'out_file', maskfunc2, 'in_file')
featpreproc.connect(dilatemask, 'out_file', maskfunc2, 'in_file2')
"""
Smooth each run using SUSAN with the brightness threshold set to 75%
of the median value for each run and a mask consituting the mean
functional
"""
smooth = create_susan_smooth()
featpreproc.connect(inputnode, 'fwhm', smooth, 'inputnode.fwhm')
featpreproc.connect(maskfunc2, 'out_file', smooth, 'inputnode.in_files')
featpreproc.connect(dilatemask, 'out_file', smooth, 'inputnode.mask_file')
"""
Mask the smoothed data with the dilated mask
"""
maskfunc3 = pe.MapNode(interface=fsl.ImageMaths(suffix='_mask',
op_string='-mas'),
iterfield=['in_file', 'in_file2'],
name='maskfunc3')
featpreproc.connect(smooth, 'outputnode.smoothed_files', maskfunc3, 'in_file')
featpreproc.connect(dilatemask, 'out_file', maskfunc3, 'in_file2')
concatnode = pe.Node(interface=util.Merge(2),
name='concat')
featpreproc.connect(maskfunc2,('out_file', tolist), concatnode, 'in1')
featpreproc.connect(maskfunc3,('out_file', tolist), concatnode, 'in2')
"""
The following nodes select 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.
"""
selectnode = pe.Node(interface=util.Select(),name='select')
featpreproc.connect(concatnode, 'out', selectnode, 'inlist')
featpreproc.connect(inputnode, ('fwhm', chooseindex), selectnode, 'index')
featpreproc.connect(selectnode, 'out', outputnode, 'smoothed_files')
"""
Scale the median value of the run is set to 10000
"""
meanscale = pe.MapNode(interface=fsl.ImageMaths(suffix='_gms'),
iterfield=['in_file','op_string'],
name='meanscale')
featpreproc.connect(selectnode, 'out', meanscale, 'in_file')
"""
Define a function to get the scaling factor for intensity normalization
"""
featpreproc.connect(medianval, ('out_stat', getmeanscale), meanscale, 'op_string')
"""
Perform temporal highpass filtering on the data
"""
if highpass:
highpass = pe.MapNode(interface=fsl.ImageMaths(suffix='_tempfilt'),
iterfield=['in_file'],
name='highpass')
featpreproc.connect(inputnode, ('highpass', highpass_operand), highpass, 'op_string')
featpreproc.connect(meanscale, 'out_file', highpass, 'in_file')
featpreproc.connect(highpass, 'out_file', outputnode, 'highpassed_files')
"""
Generate a mean functional image from the first run
"""
meanfunc3 = pe.MapNode(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
iterfield=['in_file'],
name='meanfunc3')
if highpass:
featpreproc.connect(highpass, 'out_file', meanfunc3, 'in_file')
else:
featpreproc.connect(meanscale, 'out_file', meanfunc3, 'in_file')
featpreproc.connect(meanfunc3, 'out_file', outputnode, 'mean')
return featpreproc
#Wraps command **flirt**
NodeHash_22c888c0 = pe.MapNode(interface = fsl.FLIRT(), name = 'NodeName_22c888c0', iterfield = ['in_file', 'in_matrix_file', 'reference', 'wm_seg'])
NodeHash_22c888c0.inputs.cost = 'bbr'
NodeHash_22c888c0.inputs.dof = 6
NodeHash_22c888c0.inputs.no_resample = True
#Wraps command **mcflirt**
NodeHash_32896ec0 = pe.MapNode(interface = fsl.MCFLIRT(), name = 'NodeName_32896ec0', iterfield = ['in_file', 'ref_file'])
NodeHash_32896ec0.inputs.interpolation = 'spline'
NodeHash_32896ec0.inputs.save_mats = True
NodeHash_32896ec0.inputs.save_plots = True
NodeHash_32896ec0.inputs.save_rms = True
#Wraps command **fsl_tsplot**
NodeHash_2a03f5c0 = pe.MapNode(interface = fsl.PlotMotionParams(), name = 'NodeName_2a03f5c0', iterfield = ['in_file'])
NodeHash_2a03f5c0.inputs.args = '-a x,y,z -w 640 -h 144'
NodeHash_2a03f5c0.inputs.in_source = 'fsl'
NodeHash_2a03f5c0.iterables = [('plot_type', ['rotations', 'translations'])]
#Wraps command **fslmaths**
NodeHash_22a97680 = pe.MapNode(interface = fsl.MeanImage(), name = 'NodeName_22a97680', iterfield = ['in_file'])
NodeHash_22a97680.inputs.dimension = 'T'
#Wraps command **bet**
NodeHash_55ea000 = pe.MapNode(interface = fsl.BET(), name = 'NodeName_55ea000', iterfield = ['in_file'])
NodeHash_55ea000.inputs.frac = 0.3
NodeHash_55ea000.inputs.mask = True
NodeHash_55ea000.inputs.no_output = True
#Wraps command **fslmaths**
preproc.connect(inputnode, ('func', getmiddlevolume), extract_ref, 't_min')
"""
Realign the functional runs to the middle volume of the first run
"""
motion_correct = pe.MapNode(interface=fsl.MCFLIRT(save_mats=True,
save_plots=True),
name='realign',
iterfield=['in_file'])
preproc.connect(img2float, 'out_file', motion_correct, 'in_file')
preproc.connect(extract_ref, 'roi_file', motion_correct, 'ref_file')
"""
Plot the estimated motion parameters
"""
plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
preproc.connect(motion_correct, 'par_file', plot_motion, 'in_file')
"""
Extract the mean volume of the first functional run
"""
meanfunc = pe.Node(interface=fsl.ImageMaths(op_string='-Tmean',
suffix='_mean'),
name='meanfunc')
preproc.connect(motion_correct, ('out_file', pickfirst), meanfunc, 'in_file')
"""
Strip the skull from the mean functional to generate a mask
"""
def create_motion_correction_workflow(analysis_info, name='moco'):
"""uses sub-workflows to perform different registration steps.
Requires fsl and freesurfer tools
Parameters
----------
name : string
name of workflow
Example
-------
>>> motion_correction_workflow = create_motion_correction_workflow('motion_correction_workflow')
>>> motion_correction_workflow.inputs.inputspec.output_directory = '/data/project/raw/BIDS/sj_1/'
>>> motion_correction_workflow.inputs.inputspec.in_files = ['sub-001.nii.gz','sub-002.nii.gz']
>>> motion_correction_workflow.inputs.inputspec.which_file_is_EPI_space = 'middle'
Inputs::
inputspec.output_directory : directory in which to sink the result files
inputspec.in_files : list of functional files
inputspec.which_file_is_EPI_space : determines which file is the 'standard EPI space'
Outputs::
outputspec.EPI_space_file : standard EPI space file, one timepoint
outputspec.motion_corrected_files : motion corrected files
outputspec.motion_correction_plots : motion correction plots
outputspec.motion_correction_parameters : motion correction parameters
"""
import os
import os.path as op
import nipype.pipeline as pe
import nipype.interfaces.fsl as fsl
import nipype.interfaces.utility as util
import nipype.interfaces.io as nio
from nipype.interfaces.utility import Function, IdentityInterface
import nipype.interfaces.utility as niu
########################################################################################
# nodes
########################################################################################
input_node = pe.Node(IdentityInterface(fields=[
'in_files', 'inplane_T2_files', 'T2_files_reg_matrices',
'output_directory', 'which_file_is_EPI_space', 'sub_id', 'tr'
]),
name='inputspec')
output_node = pe.Node(IdentityInterface(fields=([
'motion_corrected_files', 'EPI_space_file', 'T2_space_file',
'motion_correction_plots', 'motion_correction_parameters',
'extended_motion_correction_parameters',
'new_motion_correction_parameters'
])),
name='outputspec')
EPI_file_selector_node = pe.Node(Function(
input_names=['which_file', 'in_files'],
output_names='raw_EPI_space_file',
function=EPI_file_selector),
name='EPI_file_selector_node')
# motion_correct_EPI_space = pe.Node(interface=fsl.MCFLIRT(
# save_mats = True,
# stats_imgs = True,
# save_plots = True,
# save_rms = True,
# cost = 'normmi',
# interpolation = 'sinc',
# dof = 6,
# # ref_vol = 0
# ), name='realign_space')
# mean_bold = pe.Node(interface=fsl.maths.MeanImage(dimension='T'), name='mean_space')
# new approach, which should aid in the joint motion correction of
# multiple sessions together, by pre-registering each run.
# the strategy would be to, for each run, take the first TR
# and FLIRT-align (6dof) it to the EPI_space file.
# then we can use this as an --infile argument to mcflirt.
select_target_T2_node = pe.Node(Function(
input_names=['T2_file_list', 'target_session'],
output_names=['which_T2'],
function=select_target_T2),
name='select_target_T2_node')
select_target_T2_node.inputs.target_session = analysis_info[
'target_session']
# select_target_epi_node = pe.Node(Function(input_names=['epi_file_list', 'T2_file_list', 'target_session', 'which_file'], output_names=['target_epi'],
# function=select_target_epi), name='select_target_epi_node')
# select_target_epi_node.inputs.target_session = analysis_info['target_session']
select_T2_for_epi_node = pe.MapNode(Function(
input_names=['epi_file', 'T2_file_list'],
output_names=['which_T2_file'],
function=select_T2_for_epi),
name='select_T2_for_epi_node',
iterfield=['epi_file'])
select_T2_mat_for_epi_node = pe.MapNode(Function(
input_names=['epi_file', 'T2_file_list'],
output_names=['which_T2_file'],
function=select_T2_for_epi),
name='select_T2_mat_for_epi_node',
iterfield=['epi_file'])
bet_T2_node = pe.MapNode(interface=fsl.BET(
frac=analysis_info['T2_bet_f_value'],
vertical_gradient=analysis_info['T2_bet_g_value'],
functional=False,
mask=True),
name='bet_T2',
iterfield=['in_file'])
bet_epi_node = pe.MapNode(interface=fsl.BET(
frac=analysis_info['T2_bet_f_value'],
vertical_gradient=analysis_info['T2_bet_g_value'],
functional=True,
mask=True),
name='bet_epi',
iterfield=['in_file'])
motion_correct_all = pe.MapNode(interface=fsl.MCFLIRT(save_mats=True,
save_plots=True,
cost='normmi',
interpolation='sinc',
stats_imgs=True,
dof=6),
name='realign_all',
iterfield=['in_file', 'ref_file'])
plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
name='plot_motion',
iterfield=['in_file'])
extend_motion_pars = pe.MapNode(Function(
input_names=['moco_par_file', 'tr'],
output_names=['new_out_file', 'ext_out_file'],
function=_extend_motion_parameters),
name='extend_motion_pars',
iterfield=['moco_par_file'])
# registration node is set up for rigid-body within-modality reg
# reg_flirt_N = pe.MapNode(fsl.FLIRT(cost_func='normcorr', output_type = 'NIFTI_GZ',# dof = 6, schedule = op.abspath(op.join(os.environ['FSLDIR'], 'etc', 'flirtsch', 'sch2D_6dof')),
# interp = 'sinc', dof = 6),
# name = 'reg_flirt_N', iterfield = ['in_file'])
regapply_moco_node = pe.MapNode(interface=fsl.ApplyXfm(interp='spline'),
name='regapply_moco_node',
iterfield=['in_file', 'in_matrix_file'])
resample_epis = pe.MapNode(fsl.maths.MathsCommand(args=' -subsamp2offc '),
name='resample_epis',
iterfield=['in_file'])
resample_target_T2 = pe.Node(
fsl.maths.MathsCommand(args=' -subsamp2offc '),
name='resample_target_T2')
rename = pe.Node(niu.Rename(format_string='session_EPI_space',
keep_ext=True),
name='namer')
rename_T2 = pe.Node(niu.Rename(format_string='session_T2_space',
keep_ext=True),
name='namer_T2')
########################################################################################
# workflow
########################################################################################
motion_correction_workflow = pe.Workflow(name=name)
motion_correction_workflow.connect(input_node, 'in_files', bet_epi_node,
'in_file')
motion_correction_workflow.connect(input_node, 'inplane_T2_files',
bet_T2_node, 'in_file')
# select example func data, and example T2 space
# motion_correction_workflow.connect(input_node, 'which_file_is_EPI_space', select_target_epi_node, 'which_file')
# motion_correction_workflow.connect(bet_epi_node, 'out_file', select_target_epi_node, 'epi_file_list')
# motion_correction_workflow.connect(bet_T2_node, 'out_file', select_target_epi_node, 'T2_file_list')
motion_correction_workflow.connect(bet_T2_node, 'out_file',
select_target_T2_node, 'T2_file_list')
# motion correct and average the standard EPI file
# motion_correction_workflow.connect(select_target_epi_node, 'target_epi', motion_correct_EPI_space, 'in_file')
# motion_correction_workflow.connect(motion_correct_EPI_space, 'out_file', mean_bold, 'in_file')
# output node, for later saving
# motion_correction_workflow.connect(mean_bold, 'out_file', output_node, 'EPI_space_file')
motion_correction_workflow.connect(select_target_T2_node, 'which_T2',
output_node, 'T2_space_file')
# find the relevant T2 files for each of the epi files
motion_correction_workflow.connect(bet_epi_node, 'out_file',
select_T2_for_epi_node, 'epi_file')
motion_correction_workflow.connect(bet_T2_node, 'out_file',
select_T2_for_epi_node, 'T2_file_list')
# find the relevant T2 registration file for each of the epi files
motion_correction_workflow.connect(bet_epi_node, 'out_file',
select_T2_mat_for_epi_node, 'epi_file')
motion_correction_workflow.connect(input_node, 'T2_files_reg_matrices',
select_T2_mat_for_epi_node,
'T2_file_list')
# motion correction across runs
# motion_correction_workflow.connect(prereg_flirt_N, 'out_matrix_file', motion_correct_all, 'init')
motion_correction_workflow.connect(bet_epi_node, 'out_file',
motion_correct_all, 'in_file')
motion_correction_workflow.connect(select_T2_for_epi_node, 'which_T2_file',
motion_correct_all, 'ref_file')
# motion_correction_workflow.connect(mean_bold, 'out_file', motion_correct_all, 'ref_file')
# the registration
# motion_correction_workflow.connect(select_T2_for_epi_node, 'which_T2_file', reg_flirt_N, 'in_file')
# motion_correction_workflow.connect(select_target_T2_node, 'which_T2', reg_flirt_N, 'reference')
# output of motion correction of all files
motion_correction_workflow.connect(motion_correct_all, 'par_file',
output_node,
'motion_correction_parameters')
motion_correction_workflow.connect(motion_correct_all, 'out_file',
regapply_moco_node, 'in_file')
# registration has already been done by hand. This registration matrix is in the datasource, and applied here.
motion_correction_workflow.connect(select_T2_mat_for_epi_node,
'which_T2_file', regapply_moco_node,
'in_matrix_file')
motion_correction_workflow.connect(select_target_T2_node, 'which_T2',
regapply_moco_node, 'reference')
motion_correction_workflow.connect(regapply_moco_node, 'out_file',
resample_epis, 'in_file')
motion_correction_workflow.connect(resample_epis, 'out_file', output_node,
'motion_corrected_files')
motion_correction_workflow.connect(motion_correct_all, 'par_file',
extend_motion_pars, 'moco_par_file')
motion_correction_workflow.connect(input_node, 'tr', extend_motion_pars,
'tr')
motion_correction_workflow.connect(
extend_motion_pars, 'ext_out_file', output_node,
'extended_motion_correction_parameters')
motion_correction_workflow.connect(extend_motion_pars, 'new_out_file',
output_node,
'new_motion_correction_parameters')
motion_correction_workflow.connect(rename, 'out_file', output_node,
'EPI_space_file')
########################################################################################
# Plot the estimated motion parameters
########################################################################################
plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
motion_correction_workflow.connect(motion_correct_all, 'par_file',
plot_motion, 'in_file')
motion_correction_workflow.connect(plot_motion, 'out_file', output_node,
'motion_correction_plots')
########################################################################################
# outputs via datasink
########################################################################################
datasink = pe.Node(nio.DataSink(), name='sinker')
datasink.inputs.parameterization = False
# first link the workflow's output_directory into the datasink.
motion_correction_workflow.connect(input_node, 'output_directory',
datasink, 'base_directory')
motion_correction_workflow.connect(input_node, 'sub_id', datasink,
'container')
motion_correction_workflow.connect(select_target_T2_node, 'which_T2',
resample_target_T2, 'in_file')
motion_correction_workflow.connect(resample_target_T2, 'out_file', rename,
'in_file')
motion_correction_workflow.connect(rename, 'out_file', datasink, 'reg')
motion_correction_workflow.connect(select_target_T2_node, 'which_T2',
rename_T2, 'in_file')
motion_correction_workflow.connect(rename_T2, 'out_file', datasink,
'reg.@T2')
# motion_correction_workflow.connect(regapply_moco_node, 'out_file', datasink, 'mcf.hr')
motion_correction_workflow.connect(resample_epis, 'out_file', datasink,
'mcf')
motion_correction_workflow.connect(motion_correct_all, 'par_file',
datasink, 'mcf.motion_pars')
motion_correction_workflow.connect(plot_motion, 'out_file', datasink,
'mcf.motion_plots')
motion_correction_workflow.connect(extend_motion_pars, 'ext_out_file',
datasink, 'mcf.ext_motion_pars')
motion_correction_workflow.connect(extend_motion_pars, 'new_out_file',
datasink, 'mcf.new_motion_pars')
motion_correction_workflow.connect(bet_T2_node, 'out_file', datasink,
'mcf.T2s')
# motion_correction_workflow.connect(motion_correct_all, 'out_file', datasink, 'mcf.hr_per_session')
# motion_correction_workflow.connect(reg_flirt_N, 'out_file', datasink, 'mcf.T2_per_session')
return motion_correction_workflow