# Select WM segmentation file from segmentation output
def get_csf(files):
return files[0]
anatSegment = pe.Node(fsl.FAST(output_type='NIFTI_GZ', number_classes=3),
name='anatSegment')
# Remove initial volumes
volTrim = pe.Node(fsl.ExtractROI(t_min=numDisdaq,
t_size=-1,
output_type='NIFTI_GZ'),
name='volTrim')
# Estimate extreme motion outliers
motionOutliers = pe.Node(fsl.MotionOutliers(), name="motionOutliers")
# Estimate motion parameters
motionCorrect = pe.Node(fsl.MCFLIRT(cost='normcorr',
dof=12,
mean_vol=True,
save_plots=True,
save_rms=True,
output_type='NIFTI_GZ'),
name="motionCorrect")
# Mask motion corrected image with extracted brain mask
motionMask = pe.Node(fsl.maths.ApplyMask(output_type='NIFTI_GZ'),
name='motionMask')
# In[14]:
drop1 = Node(fsl.ExtractROI(
in_file=(func1 + '/' + subject + '_run1orient.nii.gz'),
roi_file=(func1 + '/' + subject + '_run1drop.nii.gz'),
output_type='NIFTI_GZ',
t_min=4,
t_size=247),
name='drop1')
drop1.run()
# In[15]:
motion_outliers1 = fsl.MotionOutliers(
in_file=(func1 + '/' + subject + '_run1drop.nii.gz'),
out_file=(func1 + '/' + subject + '_run1motionoutliers'))
motion_outliers1.run()
# In[16]:
func_strip1 = Node(fsl.BET(
in_file=(func1 + '/' + subject + '_run1drop.nii.gz'),
out_file=(func1 + '/' + subject + '_run1brain.nii.gz'),
frac=0.3,
functional=True),
name='func_strip')
func_strip1.run()
# In[17]:
def run_mcflirt(subj, raw_folder, motion_folder):
print("\n 1.Motion correction")
os.system('mkdir -p %s' % opj(motion_folder, subj))
mcflirt.inputs.in_file = opj(raw_folder, subj, '4D.nii')
mcflirt.inputs.out_file = opj(motion_folder, subj, '4D_static.nii.gz')
mcflirt.inputs.mean_vol = True
#mcflirt.inputs.stats_imgs = True
#mcflirt.inputs.save_plots = True
#mcflirt.inputs.stages = 4
print(mcflirt.cmdline)
os.system(mcflirt.cmdline)
motion_out = fsl.MotionOutliers()
def run_motion_outliers(subj, motion_folder):
print("\n Motion outliers")
motion_out.inputs.in_file = opj(motion_folder, subj, '4D_static.nii.gz')
motion_out.inputs.dummy = 4
motion_out.inputs.metric = 'fd'
motion_out.inputs.out_file = opj(motion_folder, subj, 'outfile.txt')
motion_out.inputs.output_type = 'NIFTI_GZ'
motion_out.inputs.out_metric_plot = opj(motion_folder, subj,
'metricplot.png')
motion_out.inputs.out_metric_values = opj(motion_folder, subj,
'metrics.txt')
print(motion_out.cmdline)
motion_out.run()
# likelihood_model='Gaussian',
# n_iterations=5,
# convergence_threshold=0.000001,
# posterior_formulation='Socrates',
# use_mixture_model_proportions=True,
# save_posteriors=True
# Remove initial volumes
volTrim = pe.Node(fsl.ExtractROI(
t_min=numDisdaq,
t_size=-1,
output_type='NIFTI_GZ'),
name='volTrim')
# Estimate extreme motion outliers
motionOutliers = pe.Node(fsl.MotionOutliers(),
name="motionOutliers")
# Estimate motion parameters
motionCorrect = pe.Node(fsl.MCFLIRT(
cost='normcorr',
dof=12,
mean_vol=True,
save_plots=True,
save_rms=True,
output_type='NIFTI_GZ'),
name="motionCorrect")
# Despike raw data
despike = pe.Node(afni.preprocess.Despike(
outputtype='NIFTI_GZ'),
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 run_workflow(session=None, csv_file=None, undist=True):
from nipype import config
#config.enable_debug_mode()
# ------------------ Specify variables
ds_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
data_dir = ds_root
output_dir = 'derivatives/featpreproc/motion_outliers'
working_dir = 'workingdirs'
# ------------------ Input Files
infosource = Node(IdentityInterface(fields=[
'subject_id',
'session_id',
'run_id',
]),
name="infosource")
if csv_file is not None:
print('=== reading csv ===')
# Read csv and use pandas to set-up image and ev-processing
df = pd.read_csv(csv_file)
# init lists
sub_img = []
ses_img = []
run_img = []
# fill lists to iterate mapnodes
for index, row in df.iterrows():
for r in row.run.strip("[]").split(" "):
sub_img.append(row.subject)
ses_img.append(row.session)
run_img.append(r)
infosource.iterables = [
('subject_id', sub_img),
('session_id', ses_img),
('run_id', run_img),
]
infosource.synchronize = True
else:
print("No csv-file specified. Don't know what data to process.")
# use undistorted epi's if these are requested (need to be generated with undistort workflow)
if undist:
func_flag = 'preproc_undistort'
else:
func_flag = 'preproc'
# SelectFiles
templates = {
'motion_outlier_files':
'derivatives/featpreproc/motion_outliers/sub-{subject_id}/'
'ses-{session_id}/func/art.sub-{subject_id}_ses-{session_id}_*_'
'run-{run_id}_bold_res-1x1x1_' + func_flag + '_mc_maths_outliers.txt',
'masks':
'derivatives/featpreproc/motion_outliers/sub-{subject_id}/'
'ses-{session_id}/func/mask.sub-{subject_id}_ses-{session_id}_*_'
'run-{run_id}_bold_res-1x1x1_' + func_flag + '_mc_maths.nii.gz',
'motion_corrected':
'derivatives/featpreproc/motion_corrected/sub-{subject_id}/'
'ses-{session_id}/func/sub-{subject_id}_ses-{session_id}_*_'
'run-{run_id}_bold_res-1x1x1_' + func_flag + '_mc.nii.gz',
}
inputfiles = Node(nio.SelectFiles(templates, base_directory=data_dir),
name="input_files")
# ------------------ Output Files
# Datasink
outputfiles = Node(nio.DataSink(base_directory=ds_root,
container=output_dir,
parameterization=True),
name="output_files")
# Use the following DataSink output substitutions
outputfiles.inputs.substitutions = [
('subject_id_', 'sub-'),
('session_id_', 'ses-'),
('run_id_', 'run-'),
('/merged_outliers/', '/'),
('/fslmotionoutlier_file/', '/'),
('bold_res-1x1x1_' + func_flag + '_mc_outliers',
func_flag + '_fslmotionoutliers'),
]
# Put result into a BIDS-like format
outputfiles.inputs.regexp_substitutions = [
(r'_run-([a-zA-Z0-9]*)_ses-([a-zA-Z0-9]*)_sub-([a-zA-Z0-9]*)',
r'/sub-\3/ses-\2/func/'),
]
# -------------------------------------------- Create Pipeline
fslmotionoutliers = Workflow(name='fslmotionoutliers',
base_dir=os.path.join(ds_root, working_dir))
fslmotionoutliers.connect([(infosource, inputfiles, [
('subject_id', 'subject_id'),
('session_id', 'session_id'),
('run_id', 'run_id'),
])])
GetOutliers = Node(fsl.MotionOutliers(), name='GetOutliers')
GetOutliers.inputs.no_motion_correction = True
fslmotionoutliers.connect(inputfiles, 'motion_corrected', GetOutliers,
'in_file')
fslmotionoutliers.connect(inputfiles, 'masks', GetOutliers, 'mask')
fslmotionoutliers.connect(GetOutliers, 'out_file', outputfiles,
'fslmotionoutlier_file')
# convert the fsl style design matrix to AFNI style volume indeces
ConvToAFNI = Node(name='ConvtoAFNI',
interface=Function(
input_names=['fslmat', 'rafile', 'undist'],
output_names=['mergedoutliers_file'],
function=combine_outlier_files,
))
fslmotionoutliers.connect(GetOutliers, 'out_file', ConvToAFNI, 'fslmat')
fslmotionoutliers.connect(inputfiles, 'motion_outlier_files', ConvToAFNI,
'rafile')
fslmotionoutliers.connect(ConvToAFNI, 'mergedoutliers_file', outputfiles,
'merged_outliers')
fslmotionoutliers.stop_on_first_crash = False # True
fslmotionoutliers.keep_inputs = True
fslmotionoutliers.remove_unnecessary_outputs = False
fslmotionoutliers.write_graph()
fslmotionoutliers.run()