def create_lemon_resting(subject, working_dir, data_dir, freesurfer_dir,
out_dir, vol_to_remove, TR, epi_resolution, highpass,
lowpass, echo_space, te_diff, pe_dir, standard_brain,
standard_brain_resampled, standard_brain_mask,
standard_brain_mask_resampled, fwhm_smoothing):
# set fsl output type to nii.gz
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# main workflow
func_preproc = Workflow(name='lemon_resting')
func_preproc.base_dir = working_dir
func_preproc.config['execution'][
'crashdump_dir'] = func_preproc.base_dir + "/crash_files"
# select files
templates = {
'func': 'func/EPI_t2.nii',
'fmap_phase': 'unwarp/B0_ph.nii',
'fmap_mag': 'unwarp/B0_mag.nii',
'anat_head':
'preprocessed/mod/anat/T1.nii.gz', #either with mod or without
'anat_brain':
'preprocessed/mod/anat/brain.nii.gz', #new version with brain_extraction from freesurfer #T1_brain_brain.nii.gz',
'brain_mask':
'preprocessed/mod/anat/T1_brain_mask.nii.gz', #T1_brain_brain_mask.nii.gz',
'ants_affine':
'preprocessed/mod/anat/transforms2mni/transform0GenericAffine.mat',
'ants_warp':
'preprocessed/mod/anat/transforms2mni/transform1Warp.nii.gz'
}
selectfiles = Node(nio.SelectFiles(templates, base_directory=data_dir),
name="selectfiles")
# node to remove first volumes
remove_vol = Node(util.Function(input_names=['in_file', 't_min'],
output_names=["out_file"],
function=strip_rois_func),
name='remove_vol')
remove_vol.inputs.t_min = vol_to_remove
# workflow for motion correction
moco = create_moco_pipeline()
# workflow for fieldmap correction and coregistration
fmap_coreg = create_fmap_coreg_pipeline()
fmap_coreg.inputs.inputnode.fs_subjects_dir = freesurfer_dir
fmap_coreg.inputs.inputnode.fs_subject_id = subject
fmap_coreg.inputs.inputnode.echo_space = echo_space
fmap_coreg.inputs.inputnode.te_diff = te_diff
fmap_coreg.inputs.inputnode.pe_dir = pe_dir
# workflow for applying transformations to timeseries
transform_ts = create_transform_pipeline()
transform_ts.inputs.inputnode.resolution = epi_resolution
#workflow to convert signal into percent signal change
normalize = create_normalize_pipeline()
normalize.inputs.inputnode.tr = TR
#workflow to transform timeseries to MNI
ants_registration = create_ants_registration_pipeline()
ants_registration.inputs.inputnode.ref = standard_brain_resampled
#workflow to smooth
smoothing = create_smoothing_pipeline()
smoothing.inputs.inputnode.fwhm = fwhm_smoothing
#workflow to correct slice timing
slicetiming = create_slice_timing_pipeline()
#visualize registration results
visualize = create_visualize_pipeline()
visualize.inputs.inputnode.mni_template = standard_brain_resampled
#sink to store files
sink = Node(nio.DataSink(
parameterization=False,
base_directory=out_dir,
substitutions=[
('fmap_phase_fslprepared', 'fieldmap'),
('fieldmap_fslprepared_fieldmap_unmasked_vsm', 'shiftmap'),
('plot.rest_coregistered', 'outlier_plot'),
('filter_motion_comp_norm_compcor_art_dmotion',
'nuissance_matrix'),
('rest_realigned.nii.gz_abs.rms', 'rest_realigned_abs.rms'),
('rest_realigned.nii.gz.par', 'rest_realigned.par'),
('rest_realigned.nii.gz_rel.rms', 'rest_realigned_rel.rms'),
('rest_realigned.nii.gz_abs_disp', 'abs_displacement_plot'),
('rest_realigned.nii.gz_rel_disp', 'rel_displacment_plot'),
('art.rest_coregistered_outliers', 'outliers'),
('global_intensity.rest_coregistered', 'global_intensity'),
('norm.rest_coregistered', 'composite_norm'),
('stats.rest_coregistered', 'stats'),
('rest_denoised_bandpassed_norm.nii.gz',
'rest_preprocessed.nii.gz'),
('rest_denoised_bandpassed_norm_trans.nii.gz', 'rest_mni.nii.gz'),
('rest2anat_masked_st_norm_trans_smooth.nii',
'rest_mni_smoothed.nii')
]),
name='sink')
# connections
func_preproc.connect([
#remove the first volumes
(selectfiles, remove_vol, [('func', 'in_file')]),
#align volumes and motion correction
(remove_vol, moco, [('out_file', 'inputnode.epi')]),
#prepare field map
(selectfiles, fmap_coreg, [('fmap_phase', 'inputnode.phase'),
('fmap_mag', 'inputnode.mag'),
('anat_head', 'inputnode.anat_head'),
('anat_brain', 'inputnode.anat_brain')]),
(moco, fmap_coreg, [('outputnode.epi_mean', 'inputnode.epi_mean')]),
(remove_vol, transform_ts, [('out_file', 'inputnode.orig_ts')]),
(selectfiles, transform_ts, [('anat_head', 'inputnode.anat_head')]),
(selectfiles, transform_ts, [('brain_mask', 'inputnode.brain_mask')]),
(moco, transform_ts, [('outputnode.mat_moco', 'inputnode.mat_moco')]),
(fmap_coreg, transform_ts, [('outputnode.fmap_fullwarp',
'inputnode.fullwarp')]),
##add slice time correction after applying motion realignement + unwarping
(transform_ts, slicetiming, [('outputnode.trans_ts_masked',
'inputnode.ts')]),
(slicetiming, normalize, [('outputnode.ts_slicetcorrected',
'inputnode.epi_coreg')]),
(normalize, ants_registration, [('outputnode.normalized_file',
'inputnode.denoised_ts')]),
#registration to MNI space
(selectfiles, ants_registration, [('ants_affine',
'inputnode.ants_affine')]),
(selectfiles, ants_registration, [('ants_warp', 'inputnode.ants_warp')
]),
(ants_registration, smoothing, [('outputnode.ants_reg_ts',
'inputnode.ts_transformed')]),
(smoothing, visualize, [('outputnode.ts_smoothed',
'inputnode.ts_transformed')]),
##all the output
(
moco,
sink,
[ #('outputnode.epi_moco', 'realign.@realigned_ts'),
('outputnode.par_moco', 'realign.@par'),
('outputnode.rms_moco', 'realign.@rms'),
('outputnode.mat_moco', 'realign.MAT.@mat'),
('outputnode.epi_mean', 'realign.@mean'),
('outputnode.rotplot', 'realign.plots.@rotplot'),
('outputnode.transplot', 'realign.plots.@transplot'),
('outputnode.dispplots', 'realign.plots.@dispplots'),
('outputnode.tsnr_file', 'realign.@tsnr')
]),
(
fmap_coreg,
sink,
[
('outputnode.fmap', 'coregister.transforms2anat.@fmap'),
#('outputnode.unwarpfield_epi2fmap', 'coregister.@unwarpfield_epi2fmap'),
('outputnode.unwarped_mean_epi2fmap',
'coregister.@unwarped_mean_epi2fmap'),
('outputnode.epi2fmap', 'coregister.@epi2fmap'),
#('outputnode.shiftmap', 'coregister.@shiftmap'),
('outputnode.fmap_fullwarp',
'coregister.transforms2anat.@fmap_fullwarp'),
('outputnode.epi2anat', 'coregister.@epi2anat'),
('outputnode.epi2anat_mat',
'coregister.transforms2anat.@epi2anat_mat'),
('outputnode.epi2anat_dat',
'coregister.transforms2anat.@epi2anat_dat'),
('outputnode.epi2anat_mincost', 'coregister.@epi2anat_mincost')
]),
(
transform_ts,
sink,
[ #('outputnode.trans_ts', 'coregister.@full_transform_ts'),
('outputnode.trans_ts_mean',
'coregister.@full_transform_mean'),
('outputnode.resamp_brain', 'coregister.@resamp_brain')
]),
(ants_registration, sink, [('outputnode.ants_reg_ts',
'ants.@antsnormalized')]),
(smoothing, sink, [('outputnode.ts_smoothed', '@smoothed.FWHM6')]),
])
#func_preproc.write_graph(dotfilename='func_preproc.dot', graph2use='colored', format='pdf', simple_form=True)
func_preproc.run()
def create_resting():
# main workflow
func_preproc = Workflow(name='resting')
inputnode = Node(util.IdentityInterface(fields=[
'subject_id', 'out_dir', 'freesurfer_dir', 'func', 'rs_mag', 'rs_ph',
'anat_head', 'anat_brain', 'anat_brain_mask', 'wmseg', 'csfseg',
'vol_to_remove', 'TR', 'highpass_freq', 'epi_resolution', 'echo_space',
'te_diff', 'fwhm', 'pe_dir', 'composite_transform', 'standard_brain',
'standard_downsampled'
]),
name='inputnode')
#Use correct subject ID from long timepoint for bbregister
def change_subject_id(subject):
import re
[subj, ses] = re.split("_", subject)
new_subject_id = subject + '.long.' + subj
return new_subject_id
change_subject_id = Node(util.Function(input_names=["subject"],
output_names=["new_subject_id"],
function=change_subject_id),
name="change_subject_id")
outputnode = Node(util.IdentityInterface(fields=[
'brain', 'brainmask', 'anat2std_transforms', 'std2anat_transforms',
'anat2std', 'anat_head', 'wmseg', 'csfseg', 'wmedge', 'subject_id'
]),
name='outputnode')
##PREPROCESSING FOR AROMA (Steps 1 - 7)
def merge_if_list(in_file):
if type(in_file) == list:
import numpy as np
import nibabel as nb
import os
from nipype.utils.filemanip import split_filename
nii1 = nb.load(in_file[0])
nii1d = nii1.get_data()
nii2 = nb.load(in_file[1])
nii2d = nii2.get_data()
x = np.concatenate((nii1d, nii2d), axis=3)
new_nii = nb.Nifti1Image(x, nii1.get_affine(), nii1.get_header())
new_nii.set_data_dtype(np.float32)
_, base, _ = split_filename(in_file[0])
nb.save(new_nii, base + "_merged.nii.gz")
return os.path.abspath(base + "_merged.nii.gz")
else:
return in_file
#if rsfmri is a list -> merge files, otherwise return single list.
merge_rs = Node(util.Function(input_names=['in_file'],
output_names=["out_file"],
function=merge_if_list),
name='merge_rs')
# node to remove first volumes
remove_vol = Node(util.Function(input_names=['in_file', 't_min'],
output_names=["out_file"],
function=strip_rois_func),
name='remove_vol')
# workflow for motion correction
moco = create_moco_pipeline()
# workflow for fieldmap correction and coregistration
fmap_coreg = create_fmap_coreg_pipeline()
# workflow for applying transformations to timeseries
transform_ts = create_transform_pipeline()
#mean intensity normalization
meanintensnorm = Node(fsl.ImageMaths(op_string='-ing 10000'),
name='meanintensnorm')
smoothing = create_smoothing_pipeline()
# connections
func_preproc.connect([
(inputnode, merge_rs, [('func', 'in_file')]),
(merge_rs, remove_vol, [('out_file', 'in_file')]),
(inputnode, remove_vol, [('vol_to_remove', 't_min')]),
(inputnode, moco, [('anat_brain_mask', 'inputnode.brainmask')]),
(remove_vol, moco, [('out_file', 'inputnode.epi')]),
(inputnode, change_subject_id, [('subject_id', 'subject')]),
(change_subject_id, fmap_coreg, [('new_subject_id',
'inputnode.fs_subject_id')]),
(inputnode, fmap_coreg, [('rs_mag', 'inputnode.mag'),
('rs_ph', 'inputnode.phase'),
('freesurfer_dir',
'inputnode.fs_subjects_dir'),
('echo_space', 'inputnode.echo_space'),
('te_diff', 'inputnode.te_diff'),
('pe_dir', 'inputnode.pe_dir'),
('anat_head', 'inputnode.anat_head'),
('anat_brain', 'inputnode.anat_brain')]),
(moco, fmap_coreg, [('outputnode.epi_mean', 'inputnode.epi_mean')]),
(remove_vol, transform_ts, [('out_file', 'inputnode.orig_ts')]),
(inputnode, transform_ts, [('anat_head', 'inputnode.anat_head')]),
(inputnode, transform_ts, [('anat_brain_mask', 'inputnode.brain_mask')
]),
(inputnode, transform_ts, [('epi_resolution', 'inputnode.resolution')
]),
(moco, transform_ts, [('outputnode.mat_moco', 'inputnode.mat_moco')]),
(fmap_coreg, transform_ts, [('outputnode.fmap_fullwarp',
'inputnode.fullwarp')]),
(transform_ts, meanintensnorm, [('outputnode.trans_ts', 'in_file')]),
(meanintensnorm, smoothing, [('out_file', 'inputnode.ts_transformed')
]),
(inputnode, smoothing, [('fwhm', 'inputnode.fwhm')])
])
##CALCULATE TRANSFORM from anatomical to standard space with FSL tools
# Anat > Standard
# register high-resolution to standard template with non-linear transform
# flirt serves as preparation for fnirt)
#reorient brain to standard (because Freesurfer space can cause problems)
reorient2std = Node(fsl.Reorient2Std(), name="reorient2std")
reorient2std_rs = Node(fsl.Reorient2Std(), name="reorient2std_rs")
reorient2std_mask = Node(fsl.Reorient2Std(), name="reorient2std_mask")
flirt_prep = Node(fsl.FLIRT(cost_func='mutualinfo', interp='trilinear'),
name='flirt_prep')
flirt_prep.inputs.interp = 'trilinear'
flirt_prep.inputs.dof = 12
fnirt = Node(fsl.FNIRT(), name='fnirt')
fnirt.inputs.field_file = True
fnirt.inputs.fieldcoeff_file = True
func_preproc.connect([
(inputnode, reorient2std, [('anat_brain', 'in_file')]),
(reorient2std, flirt_prep, [('out_file', 'in_file')]),
#(inputnode, flirt_prep, [('anat_brain', 'in_file')]),
(inputnode, flirt_prep, [('standard_brain', 'reference')]),
(flirt_prep, fnirt, [('out_matrix_file', 'affine_file')]),
(reorient2std, fnirt, [('out_file', 'in_file')]),
(inputnode, fnirt, [('standard_brain', 'ref_file')]),
])
def getcwd(subject_id):
import os
tmp = os.getcwd()
tmp = tmp[:-6]
tmp = tmp + 'ica_aroma/out' #%(subject_id)
return tmp
get_wd = Node(util.Function(input_names=['subject_id'],
output_names=["d"],
function=getcwd),
name='get_wd')
ica_aroma = Node(ICA_AROMA(), name="ica_aroma")
ica_aroma.inputs.denoise_type = 'both'
#ica_aroma.inputs.out_dir = os.getcwd()
func_preproc.connect([
(moco, ica_aroma, [('outputnode.par_moco', 'motion_parameters')]),
(smoothing, reorient2std_rs, [('outputnode.ts_smoothed', 'in_file')]),
(reorient2std_rs, ica_aroma, [('out_file', 'in_file')]),
(fnirt, ica_aroma, [('field_file', 'fnirt_warp_file')]),
(transform_ts, reorient2std_mask, [('outputnode.comb_mask_resamp',
'in_file')]),
(reorient2std_mask, ica_aroma, [('out_file', 'mask')]),
(inputnode, get_wd, [('subject_id', 'subject_id')]),
(get_wd, ica_aroma, [('d', 'out_dir')])
])
##POSTPROCESSING
postprocess = create_denoise_pipeline()
func_preproc.connect([
(reorient2std_mask, postprocess, [
('out_file', 'inputnode.brain_mask')
]), #use the correctly oriented mask
(ica_aroma, postprocess, [
('nonaggr_denoised_file', 'inputnode.epi_coreg')
]), #use the nonaggr_denoised_file
(inputnode, postprocess, [('TR', 'inputnode.tr')]),
(inputnode, postprocess, [('highpass_freq', 'inputnode.highpass_freq')
]),
(inputnode, postprocess, [('wmseg', 'inputnode.wmseg')]),
(inputnode, postprocess, [('csfseg', 'inputnode.csfseg')]),
])
#outputnode
outputnode = Node(util.IdentityInterface(fields=[
'par', 'rms', 'mean_epi', 'tsnr', 'stddev_file', 'realigned_ts',
'fmap', 'unwarped_mean_epi2fmap', 'coregistered_epi2fmap',
'fmap_fullwarp', 'epi2anat', 'epi2anat_mat', 'epi2anat_dat',
'epi2anat_mincost', 'full_transform_ts', 'full_transform_mean',
'resamp_t1', 'comb_mask_resamp', 'dvars_file', 'out_flirt_prep',
'out_matrix_flirt_prep', 'out_warped', 'out_warp_field',
'aggr_denoised_file', 'nonaggr_denoised_file', 'out_dir', 'wmcsf_mask',
'combined_motion', 'comp_regressor', 'comp_F', 'comp_pF', 'out_betas',
'ts_fullspectrum', 'ts_filtered'
]),
name='outputnode')
# connections
func_preproc.connect([
(
moco,
outputnode,
[ #('outputnode.epi_moco', 'realign.@realigned_ts'),
('outputnode.par_moco', 'par'),
('outputnode.rms_moco', 'rms'),
('outputnode.epi_moco', 'realigned_ts'),
('outputnode.epi_mean', 'mean_epi'),
('outputnode.tsnr_file', 'tsnr'),
('outputnode.stddev_file', 'stddev'),
]),
(fmap_coreg, outputnode,
[('outputnode.fmap', 'fmap'),
('outputnode.unwarped_mean_epi2fmap', 'unwarped_mean_epi2fmap'),
('outputnode.epi2fmap', 'coregistered_epi2fmap'),
('outputnode.fmap_fullwarp', 'fmap_fullwarp'),
('outputnode.epi2anat', 'epi2anat'),
('outputnode.epi2anat_mat', 'epi2anat_mat'),
('outputnode.epi2anat_dat', 'epi2anat_dat'),
('outputnode.epi2anat_mincost', 'epi2anat_mincost')]),
(transform_ts, outputnode,
[('outputnode.trans_ts', 'full_transform_ts'),
('outputnode.trans_ts_mean', 'full_transform_mean'),
('outputnode.resamp_t1', 'resamp_t1'),
('outputnode.comb_mask_resamp', 'comb_mask_resamp'),
('outputnode.out_dvars', 'dvars_file')]),
(flirt_prep, outputnode, [('out_file', 'out_flirt_prep'),
('out_matrix_file', 'out_matrix_flirt_prep')
]),
(fnirt, outputnode, [('warped_file', 'out_warped'),
('field_file', 'out_warp_field')]),
(ica_aroma, outputnode, [('aggr_denoised_file', 'aggr_denoised_file'),
('nonaggr_denoised_file',
'nonaggr_denoised_file'),
('out_dir', 'out_dir')]),
(postprocess, outputnode,
[('outputnode.wmcsf_mask', 'wmcsf_mask'),
('outputnode.combined_motion', 'combined_motion'),
('outputnode.comp_regressor', 'comp_regressor'),
('outputnode.comp_F', 'comp_F'), ('outputnode.comp_pF', 'comp_pF'),
('outputnode.out_betas', 'out_betas'),
('outputnode.ts_fullspectrum', 'ts_fullspectrum'),
('outputnode.ts_filtered', 'ts_filtered')])
])
return func_preproc
def create_lemon_resting(subject, working_dir, data_dir, freesurfer_dir, out_dir,
vol_to_remove, TR, epi_resolution, highpass, lowpass,
echo_space, te_diff, pe_dir, standard_brain, standard_brain_resampled, standard_brain_mask,
standard_brain_mask_resampled, fwhm_smoothing):
# set fsl output type to nii.gz
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# main workflow
func_preproc = Workflow(name='lemon_resting')
func_preproc.base_dir = working_dir
func_preproc.config['execution']['crashdump_dir'] = func_preproc.base_dir + "/crash_files"
# select files
templates = {'func': 'raw_data/{subject}/func/EPI_t2.nii',
'fmap_phase': 'raw_data/{subject}/unwarp/B0_ph.nii',
'fmap_mag': 'raw_data/{subject}/unwarp/B0_mag.nii',
'anat_head': 'preprocessed/{subject}/structural/T1.nii.gz', # either with mod or without
'anat_brain': 'preprocessed/{subject}/structural/brain.nii.gz',
# new version with brain_extraction from freesurfer #T1_brain_brain.nii.gz',
'brain_mask': 'preprocessed/{subject}/structural/T1_brain_mask.nii.gz', # T1_brain_brain_mask.nii.gz',
'ants_affine': 'preprocessed/{subject}/structural/transforms2mni/transform0GenericAffine.mat',
'ants_warp': 'preprocessed/{subject}/structural/transforms2mni/transform1Warp.nii.gz'
}
selectfiles = Node(nio.SelectFiles(templates,
base_directory=data_dir),
name="selectfiles")
selectfiles.inputs.subject = subject
# node to remove first volumes
remove_vol = Node(util.Function(input_names=['in_file', 't_min'],
output_names=["out_file"],
function=strip_rois_func),
name='remove_vol')
remove_vol.inputs.t_min = vol_to_remove
# workflow for motion correction
moco = create_moco_pipeline()
# workflow for fieldmap correction and coregistration
fmap_coreg = create_fmap_coreg_pipeline()
fmap_coreg.inputs.inputnode.fs_subjects_dir = freesurfer_dir
fmap_coreg.inputs.inputnode.fs_subject_id = subject
fmap_coreg.inputs.inputnode.echo_space = echo_space
fmap_coreg.inputs.inputnode.te_diff = te_diff
fmap_coreg.inputs.inputnode.pe_dir = pe_dir
# workflow for applying transformations to timeseries
transform_ts = create_transform_pipeline()
transform_ts.inputs.inputnode.resolution = epi_resolution
# workflow to denoise timeseries
denoise = create_denoise_pipeline()
denoise.inputs.inputnode.highpass_sigma = 1. / (2 * TR * highpass)
denoise.inputs.inputnode.lowpass_sigma = 1. / (2 * TR * lowpass)
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1205&L=FSL&P=R57592&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4
denoise.inputs.inputnode.tr = TR
# workflow to transform timeseries to MNI
ants_registration = create_ants_registration_pipeline()
ants_registration.inputs.inputnode.ref = standard_brain_resampled
ants_registration.inputs.inputnode.tr_sec = TR
# FL added fullspectrum
# workflow to transform fullspectrum timeseries to MNI
ants_registration_full = create_ants_registration_pipeline('ants_registration_full')
ants_registration_full.inputs.inputnode.ref = standard_brain_resampled
ants_registration_full.inputs.inputnode.tr_sec = TR
# workflow to smooth
smoothing = create_smoothing_pipeline()
smoothing.inputs.inputnode.fwhm = fwhm_smoothing
# visualize registration results
visualize = create_visualize_pipeline()
visualize.inputs.inputnode.mni_template = standard_brain_resampled
# sink to store files
sink = Node(nio.DataSink(parameterization=False,
base_directory=out_dir,
substitutions=[('fmap_phase_fslprepared', 'fieldmap'),
('fieldmap_fslprepared_fieldmap_unmasked_vsm', 'shiftmap'),
('plot.rest_coregistered', 'outlier_plot'),
('filter_motion_comp_norm_compcor_art_dmotion', 'nuissance_matrix'),
('rest_realigned.nii.gz_abs.rms', 'rest_realigned_abs.rms'),
('rest_realigned.nii.gz.par', 'rest_realigned.par'),
('rest_realigned.nii.gz_rel.rms', 'rest_realigned_rel.rms'),
('rest_realigned.nii.gz_abs_disp', 'abs_displacement_plot'),
('rest_realigned.nii.gz_rel_disp', 'rel_displacment_plot'),
('art.rest_coregistered_outliers', 'outliers'),
('global_intensity.rest_coregistered', 'global_intensity'),
('norm.rest_coregistered', 'composite_norm'),
('stats.rest_coregistered', 'stats'),
('rest_denoised_bandpassed_norm.nii.gz',
'rest_preprocessed_nativespace.nii.gz'),
('rest_denoised_bandpassed_norm_trans.nii.gz',
'rest_mni_unsmoothed.nii.gz'),
('rest_denoised_bandpassed_norm_trans_smooth.nii',
'rest_mni_smoothed.nii'),
# FL added
('rest2anat_masked.nii.gz', 'rest_coregistered_nativespace.nii.gz'),
('rest2anat_denoised.nii.gz',
'rest_preprocessed_nativespace_fullspectrum.nii.gz'),
('rest2anat_denoised_trans.nii.gz',
'rest_mni_unsmoothed_fullspectrum.nii.gz')
]),
name='sink')
# connections
func_preproc.connect([
# remove the first volumes
(selectfiles, remove_vol, [('func', 'in_file')]),
# align volumes and motion correction
(remove_vol, moco, [('out_file', 'inputnode.epi')]),
# prepare field map
(selectfiles, fmap_coreg, [('fmap_phase', 'inputnode.phase'),
('fmap_mag', 'inputnode.mag'),
('anat_head', 'inputnode.anat_head'),
('anat_brain', 'inputnode.anat_brain')
]),
(moco, fmap_coreg, [('outputnode.epi_mean', 'inputnode.epi_mean')]),
# transform timeseries
(remove_vol, transform_ts, [('out_file', 'inputnode.orig_ts')]),
(selectfiles, transform_ts, [('anat_head', 'inputnode.anat_head')]),
(selectfiles, transform_ts, [('brain_mask', 'inputnode.brain_mask')]),
(moco, transform_ts, [('outputnode.mat_moco', 'inputnode.mat_moco')]),
(fmap_coreg, transform_ts, [('outputnode.fmap_fullwarp', 'inputnode.fullwarp')]),
# correct slicetiming
# FIXME slice timing?
# (transform_ts, slicetiming, [('outputnode.trans_ts_masked', 'inputnode.ts')]),
# (slicetiming, denoise, [('outputnode.ts_slicetcorrected', 'inputnode.epi_coreg')]),
(transform_ts, denoise, [('outputnode.trans_ts_masked', 'inputnode.epi_coreg')]),
# denoise data
(selectfiles, denoise, [('brain_mask', 'inputnode.brain_mask'),
('anat_brain', 'inputnode.anat_brain')]),
(moco, denoise, [('outputnode.par_moco', 'inputnode.moco_par')]),
(fmap_coreg, denoise, [('outputnode.epi2anat_dat', 'inputnode.epi2anat_dat'),
('outputnode.unwarped_mean_epi2fmap', 'inputnode.unwarped_mean')]),
(denoise, ants_registration, [('outputnode.normalized_file', 'inputnode.denoised_ts')]),
# registration to MNI space
(selectfiles, ants_registration, [('ants_affine', 'inputnode.ants_affine')]),
(selectfiles, ants_registration, [('ants_warp', 'inputnode.ants_warp')]),
# FL added fullspectrum
(denoise, ants_registration_full, [('outputnode.ts_fullspectrum', 'inputnode.denoised_ts')]),
(selectfiles, ants_registration_full, [('ants_affine', 'inputnode.ants_affine')]),
(selectfiles, ants_registration_full, [('ants_warp', 'inputnode.ants_warp')]),
(ants_registration, smoothing, [('outputnode.ants_reg_ts', 'inputnode.ts_transformed')]),
(smoothing, visualize, [('outputnode.ts_smoothed', 'inputnode.ts_transformed')]),
##all the output
(moco, sink, [ # ('outputnode.epi_moco', 'realign.@realigned_ts'),
('outputnode.par_moco', 'realign.@par'),
('outputnode.rms_moco', 'realign.@rms'),
('outputnode.mat_moco', 'realign.MAT.@mat'),
('outputnode.epi_mean', 'realign.@mean'),
('outputnode.rotplot', 'realign.plots.@rotplot'),
('outputnode.transplot', 'realign.plots.@transplot'),
('outputnode.dispplots', 'realign.plots.@dispplots'),
('outputnode.tsnr_file', 'realign.@tsnr')]),
(fmap_coreg, sink, [('outputnode.fmap', 'coregister.transforms2anat.@fmap'),
# ('outputnode.unwarpfield_epi2fmap', 'coregister.@unwarpfield_epi2fmap'),
('outputnode.unwarped_mean_epi2fmap', 'coregister.@unwarped_mean_epi2fmap'),
('outputnode.epi2fmap', 'coregister.@epi2fmap'),
# ('outputnode.shiftmap', 'coregister.@shiftmap'),
('outputnode.fmap_fullwarp', 'coregister.transforms2anat.@fmap_fullwarp'),
('outputnode.epi2anat', 'coregister.@epi2anat'),
('outputnode.epi2anat_mat', 'coregister.transforms2anat.@epi2anat_mat'),
('outputnode.epi2anat_dat', 'coregister.transforms2anat.@epi2anat_dat'),
('outputnode.epi2anat_mincost', 'coregister.@epi2anat_mincost')
]),
(transform_ts, sink, [('outputnode.trans_ts_masked', 'coregister.@full_transform_ts'),
('outputnode.trans_ts_mean', 'coregister.@full_transform_mean'),
('outputnode.resamp_brain', 'coregister.@resamp_brain')]),
(denoise, sink, [
('outputnode.wmcsf_mask', 'denoise.mask.@wmcsf_masks'),
('outputnode.combined_motion', 'denoise.artefact.@combined_motion'),
('outputnode.outlier_files', 'denoise.artefact.@outlier'),
('outputnode.intensity_files', 'denoise.artefact.@intensity'),
('outputnode.outlier_stats', 'denoise.artefact.@outlierstats'),
('outputnode.outlier_plots', 'denoise.artefact.@outlierplots'),
('outputnode.mc_regressor', 'denoise.regress.@mc_regressor'),
('outputnode.comp_regressor', 'denoise.regress.@comp_regressor'),
('outputnode.mc_F', 'denoise.regress.@mc_F'),
('outputnode.mc_pF', 'denoise.regress.@mc_pF'),
('outputnode.comp_F', 'denoise.regress.@comp_F'),
('outputnode.comp_pF', 'denoise.regress.@comp_pF'),
('outputnode.brain_mask_resamp', 'denoise.mask.@brain_resamp'),
('outputnode.brain_mask2epi', 'denoise.mask.@brain_mask2epi'),
('outputnode.normalized_file', 'denoise.@normalized'),
# FL added fullspectrum
('outputnode.ts_fullspectrum', 'denoise.@ts_fullspectrum')
]),
(ants_registration, sink, [('outputnode.ants_reg_ts', 'ants.@antsnormalized')]),
(ants_registration_full, sink, [('outputnode.ants_reg_ts', 'ants.@antsnormalized_fullspectrum')]),
(smoothing, sink, [('outputnode.ts_smoothed', '@smoothed.FWHM6')]),
])
func_preproc.write_graph(dotfilename='func_preproc.dot', graph2use='colored', format='pdf', simple_form=True)
func_preproc.run(plugin='CondorDAGMan', plugin_args={'initial_specs': 'request_memory = 1500'})
def create_resting():
# main workflow
func_preproc = Workflow(name='resting')
inputnode = Node(util.IdentityInterface(fields=[
'subject', 'out_dir', 'freesurfer_dir', 'func', 'fmap_mag',
'fmap_phase', 'anat_head', 'anat_brain', 'anat_brain_mask',
'vol_to_remove', 'TR', 'epi_resolution', 'echo_space', 'te_diff',
'pe_dir'
]),
name='inputnode')
# node to remove first volumes
remove_vol = Node(util.Function(input_names=['in_file', 't_min'],
output_names=["out_file"],
function=strip_rois_func),
name='remove_vol')
# workflow for motion correction
moco = create_moco_pipeline()
# workflow for fieldmap correction and coregistration
#have to rename subject for fu
def rename_subject_for_fu(input_id):
output_id = input_id + "_fu"
return output_id
#modify subject name so it can be saved in the same folder as other LIFE- freesurfer data
rename = Node(util.Function(input_names=['input_id'],
output_names=['output_id'],
function=rename_subject_for_fu),
name="rename")
fmap_coreg = create_fmap_coreg_pipeline()
# workflow for applying transformations to timeseries
transform_ts = create_transform_pipeline()
#detrending
detrend = Node(afni.Detrend(), name="detrend")
detrend.inputs.args = '-polort 2'
detrend.inputs.outputtype = "NIFTI"
#outputnode
outputnode = Node(util.IdentityInterface(fields=[
'par', 'rms', 'mean_epi', 'tsnr', 'fmap', 'unwarped_mean_epi2fmap',
'coregistered_epi2fmap', 'fmap_fullwarp', 'epi2anat', 'epi2anat_mat',
'epi2anat_dat', 'epi2anat_mincost', 'full_transform_ts',
'full_transform_mean', 'resamp_brain', 'detrended_epi'
]),
name='outputnode')
# connections
func_preproc.connect([
#remove the first volumes
(inputnode, remove_vol, [('func', 'in_file')]),
(inputnode, remove_vol, [('vol_to_remove', 't_min')]),
#align volumes and motion correction
(remove_vol, moco, [('out_file', 'inputnode.epi')]),
#prepare field map
(inputnode, rename, [('subject', 'input_id')]),
(rename, fmap_coreg, [('output_id', 'inputnode.fs_subject_id')]),
(inputnode, fmap_coreg, [('fmap_phase', 'inputnode.phase'),
('freesurfer_dir',
'inputnode.fs_subjects_dir'),
('echo_space', 'inputnode.echo_space'),
('te_diff', 'inputnode.te_diff'),
('pe_dir', 'inputnode.pe_dir'),
('fmap_mag', 'inputnode.mag'),
('anat_head', 'inputnode.anat_head'),
('anat_brain', 'inputnode.anat_brain')]),
(moco, fmap_coreg, [('outputnode.epi_mean', 'inputnode.epi_mean')]),
#transform ts
(remove_vol, transform_ts, [('out_file', 'inputnode.orig_ts')]),
(inputnode, transform_ts, [('anat_head', 'inputnode.anat_head')]),
(inputnode, transform_ts, [('anat_brain_mask', 'inputnode.brain_mask')
]),
(inputnode, transform_ts, [('epi_resolution', 'inputnode.resolution')
]),
(moco, transform_ts, [('outputnode.mat_moco', 'inputnode.mat_moco')]),
(fmap_coreg, transform_ts, [('outputnode.fmap_fullwarp',
'inputnode.fullwarp')]),
(transform_ts, detrend, [('outputnode.trans_ts', 'in_file')]),
##all the output
(
moco,
outputnode,
[ #('outputnode.epi_moco', 'realign.@realigned_ts'),
('outputnode.par_moco', 'par'), ('outputnode.rms_moco', 'rms'),
('outputnode.epi_mean', 'mean_epi'),
('outputnode.tsnr_file', 'tsnr')
]),
(fmap_coreg, outputnode,
[('outputnode.fmap', 'fmap'),
('outputnode.unwarped_mean_epi2fmap', 'unwarped_mean_epi2fmap'),
('outputnode.epi2fmap', 'coregistered_epi2fmap'),
('outputnode.fmap_fullwarp', 'fmap_fullwarp'),
('outputnode.epi2anat', 'epi2anat'),
('outputnode.epi2anat_mat', 'epi2anat_mat'),
('outputnode.epi2anat_dat', 'epi2anat_dat'),
('outputnode.epi2anat_mincost', 'epi2anat_mincost')]),
(transform_ts, outputnode,
[('outputnode.trans_ts', 'full_transform_ts'),
('outputnode.trans_ts_mean', 'full_transform_mean'),
('outputnode.resamp_brain', 'resamp_brain')]),
(detrend, outputnode, [('out_file', 'detrended_epi')])
])
return func_preproc
def create_lemon_resting(
subject,
working_dir,
data_dir,
freesurfer_dir,
out_dir,
vol_to_remove,
TR,
epi_resolution,
highpass,
lowpass,
echo_space,
te_diff,
pe_dir,
standard_brain,
standard_brain_resampled,
standard_brain_mask,
standard_brain_mask_resampled,
fwhm_smoothing,
):
# set fsl output type to nii.gz
fsl.FSLCommand.set_default_output_type("NIFTI_GZ")
# main workflow
func_preproc = Workflow(name="lemon_resting")
func_preproc.base_dir = working_dir
func_preproc.config["execution"]["crashdump_dir"] = func_preproc.base_dir + "/crash_files"
# select files
templates = {
"func": "func/EPI_t2.nii",
"fmap_phase": "unwarp/B0_ph.nii",
"fmap_mag": "unwarp/B0_mag.nii",
"anat_head": "preprocessed/mod/anat/T1.nii.gz", # either with mod or without
"anat_brain": "preprocessed/mod/anat/brain.nii.gz", # new version with brain_extraction from freesurfer #T1_brain_brain.nii.gz',
"brain_mask": "preprocessed/mod/anat/T1_brain_mask.nii.gz", # T1_brain_brain_mask.nii.gz',
"ants_affine": "preprocessed/mod/anat/transforms2mni/transform0GenericAffine.mat",
"ants_warp": "preprocessed/mod/anat/transforms2mni/transform1Warp.nii.gz",
}
selectfiles = Node(nio.SelectFiles(templates, base_directory=data_dir), name="selectfiles")
# node to remove first volumes
remove_vol = Node(
util.Function(input_names=["in_file", "t_min"], output_names=["out_file"], function=strip_rois_func),
name="remove_vol",
)
remove_vol.inputs.t_min = vol_to_remove
# workflow for motion correction
moco = create_moco_pipeline()
# workflow for fieldmap correction and coregistration
fmap_coreg = create_fmap_coreg_pipeline()
fmap_coreg.inputs.inputnode.fs_subjects_dir = freesurfer_dir
fmap_coreg.inputs.inputnode.fs_subject_id = subject
fmap_coreg.inputs.inputnode.echo_space = echo_space
fmap_coreg.inputs.inputnode.te_diff = te_diff
fmap_coreg.inputs.inputnode.pe_dir = pe_dir
# workflow for applying transformations to timeseries
transform_ts = create_transform_pipeline()
transform_ts.inputs.inputnode.resolution = epi_resolution
# workflow to convert signal into percent signal change
normalize = create_normalize_pipeline()
normalize.inputs.inputnode.tr = TR
# workflow to transform timeseries to MNI
ants_registration = create_ants_registration_pipeline()
ants_registration.inputs.inputnode.ref = standard_brain_resampled
# workflow to smooth
smoothing = create_smoothing_pipeline()
smoothing.inputs.inputnode.fwhm = fwhm_smoothing
# workflow to correct slice timing
slicetiming = create_slice_timing_pipeline()
# visualize registration results
visualize = create_visualize_pipeline()
visualize.inputs.inputnode.mni_template = standard_brain_resampled
# sink to store files
sink = Node(
nio.DataSink(
parameterization=False,
base_directory=out_dir,
substitutions=[
("fmap_phase_fslprepared", "fieldmap"),
("fieldmap_fslprepared_fieldmap_unmasked_vsm", "shiftmap"),
("plot.rest_coregistered", "outlier_plot"),
("filter_motion_comp_norm_compcor_art_dmotion", "nuissance_matrix"),
("rest_realigned.nii.gz_abs.rms", "rest_realigned_abs.rms"),
("rest_realigned.nii.gz.par", "rest_realigned.par"),
("rest_realigned.nii.gz_rel.rms", "rest_realigned_rel.rms"),
("rest_realigned.nii.gz_abs_disp", "abs_displacement_plot"),
("rest_realigned.nii.gz_rel_disp", "rel_displacment_plot"),
("art.rest_coregistered_outliers", "outliers"),
("global_intensity.rest_coregistered", "global_intensity"),
("norm.rest_coregistered", "composite_norm"),
("stats.rest_coregistered", "stats"),
("rest_denoised_bandpassed_norm.nii.gz", "rest_preprocessed.nii.gz"),
("rest_denoised_bandpassed_norm_trans.nii.gz", "rest_mni.nii.gz"),
("rest2anat_masked_st_norm_trans_smooth.nii", "rest_mni_smoothed.nii"),
],
),
name="sink",
)
# connections
func_preproc.connect(
[
# remove the first volumes
(selectfiles, remove_vol, [("func", "in_file")]),
# align volumes and motion correction
(remove_vol, moco, [("out_file", "inputnode.epi")]),
# prepare field map
(
selectfiles,
fmap_coreg,
[
("fmap_phase", "inputnode.phase"),
("fmap_mag", "inputnode.mag"),
("anat_head", "inputnode.anat_head"),
("anat_brain", "inputnode.anat_brain"),
],
),
(moco, fmap_coreg, [("outputnode.epi_mean", "inputnode.epi_mean")]),
(remove_vol, transform_ts, [("out_file", "inputnode.orig_ts")]),
(selectfiles, transform_ts, [("anat_head", "inputnode.anat_head")]),
(selectfiles, transform_ts, [("brain_mask", "inputnode.brain_mask")]),
(moco, transform_ts, [("outputnode.mat_moco", "inputnode.mat_moco")]),
(fmap_coreg, transform_ts, [("outputnode.fmap_fullwarp", "inputnode.fullwarp")]),
##add slice time correction after applying motion realignement + unwarping
(transform_ts, slicetiming, [("outputnode.trans_ts_masked", "inputnode.ts")]),
(slicetiming, normalize, [("outputnode.ts_slicetcorrected", "inputnode.epi_coreg")]),
(normalize, ants_registration, [("outputnode.normalized_file", "inputnode.denoised_ts")]),
# registration to MNI space
(selectfiles, ants_registration, [("ants_affine", "inputnode.ants_affine")]),
(selectfiles, ants_registration, [("ants_warp", "inputnode.ants_warp")]),
(ants_registration, smoothing, [("outputnode.ants_reg_ts", "inputnode.ts_transformed")]),
(smoothing, visualize, [("outputnode.ts_smoothed", "inputnode.ts_transformed")]),
##all the output
(
moco,
sink,
[ # ('outputnode.epi_moco', 'realign.@realigned_ts'),
("outputnode.par_moco", "realign.@par"),
("outputnode.rms_moco", "realign.@rms"),
("outputnode.mat_moco", "realign.MAT.@mat"),
("outputnode.epi_mean", "realign.@mean"),
("outputnode.rotplot", "realign.plots.@rotplot"),
("outputnode.transplot", "realign.plots.@transplot"),
("outputnode.dispplots", "realign.plots.@dispplots"),
("outputnode.tsnr_file", "realign.@tsnr"),
],
),
(
fmap_coreg,
sink,
[
("outputnode.fmap", "coregister.transforms2anat.@fmap"),
# ('outputnode.unwarpfield_epi2fmap', 'coregister.@unwarpfield_epi2fmap'),
("outputnode.unwarped_mean_epi2fmap", "coregister.@unwarped_mean_epi2fmap"),
("outputnode.epi2fmap", "coregister.@epi2fmap"),
# ('outputnode.shiftmap', 'coregister.@shiftmap'),
("outputnode.fmap_fullwarp", "coregister.transforms2anat.@fmap_fullwarp"),
("outputnode.epi2anat", "coregister.@epi2anat"),
("outputnode.epi2anat_mat", "coregister.transforms2anat.@epi2anat_mat"),
("outputnode.epi2anat_dat", "coregister.transforms2anat.@epi2anat_dat"),
("outputnode.epi2anat_mincost", "coregister.@epi2anat_mincost"),
],
),
(
transform_ts,
sink,
[ # ('outputnode.trans_ts', 'coregister.@full_transform_ts'),
("outputnode.trans_ts_mean", "coregister.@full_transform_mean"),
("outputnode.resamp_brain", "coregister.@resamp_brain"),
],
),
(ants_registration, sink, [("outputnode.ants_reg_ts", "ants.@antsnormalized")]),
(smoothing, sink, [("outputnode.ts_smoothed", "@smoothed.FWHM6")]),
]
)
# func_preproc.write_graph(dotfilename='func_preproc.dot', graph2use='colored', format='pdf', simple_form=True)
func_preproc.run()
def create_resting(subject, working_dir, data_dir, freesurfer_dir, out_dir,
vol_to_remove, TR, epi_resolution, highpass, lowpass,
echo_space, pe_dir, standard_brain, standard_brain_resampled, standard_brain_mask,
standard_brain_mask_resampled, fwhm_smoothing):
# set fsl output type to nii.gz
fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
# main workflow
func_preproc = Workflow(name='lemon_resting')
func_preproc.base_dir = working_dir
func_preproc.config['execution']['crashdump_dir'] = func_preproc.base_dir + "/crash_files"
# select files
templates = {'func': 'raw/{subject}/func/EPI_t2.nii',
'ap': 'raw/{subject}/topup/se.nii',
'pa': 'raw/{subject}/topup/seinv_ph.nii',
'anat_head': 'preprocessing/preprocessed/{subject}/structural/T1.nii.gz',
'anat_brain': 'preprocessing/preprocessed/{subject}/structural/brain.nii.gz',
'brain_mask': 'preprocessing/preprocessed/{subject}/structural/T1_brain_mask.nii.gz',
'ants_affine': 'preprocessing/preprocessed/{subject}/structural/transforms2mni/transform0GenericAffine.mat',
'ants_warp': 'preprocessing/preprocessed/{subject}/structural/transforms2mni/transform1Warp.nii.gz'
}
selectfiles = Node(nio.SelectFiles(templates,
base_directory=data_dir),
name="selectfiles")
selectfiles.inputs.subject = subject
# node to remove first volumes
remove_vol = Node(util.Function(input_names=['in_file', 't_min'],
output_names=["out_file"],
function=strip_rois_func),
name='remove_vol')
remove_vol.inputs.t_min = vol_to_remove
# workflow for motion correction
moco = create_moco_pipeline()
# workflow for fieldmap correction and coregistration
topup_coreg = create_topup_coreg_pipeline()
topup_coreg.inputs.inputnode.fs_subjects_dir = freesurfer_dir
topup_coreg.inputs.inputnode.fs_subject_id = subject
topup_coreg.inputs.inputnode.echo_space = echo_space
topup_coreg.inputs.inputnode.pe_dir = pe_dir
# workflow for applying transformations to timeseries
transform_ts = create_transform_pipeline()
transform_ts.inputs.inputnode.resolution = epi_resolution
# workflow to denoise timeseries
denoise = create_denoise_pipeline()
denoise.inputs.inputnode.highpass_sigma = 1. / (2 * TR * highpass)
denoise.inputs.inputnode.lowpass_sigma = 1. / (2 * TR * lowpass)
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1205&L=FSL&P=R57592&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4
denoise.inputs.inputnode.tr = TR
# workflow to transform timeseries to MNI
ants_registration = create_ants_registration_pipeline()
ants_registration.inputs.inputnode.ref = standard_brain
ants_registration.inputs.inputnode.tr_sec = TR
# FL added fullspectrum
# workflow to transform fullspectrum timeseries to MNI
ants_registration_full = create_ants_registration_pipeline('ants_registration_full')
ants_registration_full.inputs.inputnode.ref = standard_brain
ants_registration_full.inputs.inputnode.tr_sec = TR
# workflow to smooth
smoothing = create_smoothing_pipeline()
smoothing.inputs.inputnode.fwhm = fwhm_smoothing
# visualize registration results
visualize = create_visualize_pipeline()
visualize.inputs.inputnode.mni_template = standard_brain
# sink to store files
sink = Node(nio.DataSink(parameterization=False,
base_directory=out_dir,
substitutions=[('fmap_phase_fslprepared', 'fieldmap'),
('fieldmap_fslprepared_fieldmap_unmasked_vsm', 'shiftmap'),
('plot.rest_coregistered', 'outlier_plot'),
('filter_motion_comp_norm_compcor_art_dmotion', 'nuissance_matrix'),
('rest_realigned.nii.gz_abs.rms', 'rest_realigned_abs.rms'),
('rest_realigned.nii.gz.par', 'rest_realigned.par'),
('rest_realigned.nii.gz_rel.rms', 'rest_realigned_rel.rms'),
('rest_realigned.nii.gz_abs_disp', 'abs_displacement_plot'),
('rest_realigned.nii.gz_rel_disp', 'rel_displacment_plot'),
('art.rest_coregistered_outliers', 'outliers'),
('global_intensity.rest_coregistered', 'global_intensity'),
('norm.rest_coregistered', 'composite_norm'),
('stats.rest_coregistered', 'stats'),
('rest_denoised_bandpassed_norm.nii.gz',
'rest_preprocessed_nativespace.nii.gz'),
('rest_denoised_bandpassed_norm_trans.nii.gz',
'rest_mni_unsmoothed.nii.gz'),
('rest_denoised_bandpassed_norm_trans_smooth.nii',
'rest_mni_smoothed.nii'),
# FL added
('rest2anat_masked.nii.gz', 'rest_coregistered_nativespace.nii.gz'),
('rest2anat_denoised.nii.gz',
'rest_preprocessed_nativespace_fullspectrum.nii.gz'),
('rest2anat_denoised_trans.nii.gz',
'rest_mni_unsmoothed_fullspectrum.nii.gz')
]),
name='sink')
# connections
func_preproc.connect([
# remove the first volumes
(selectfiles, remove_vol, [('func', 'in_file')]),
# align volumes and motion correction
(remove_vol, moco, [('out_file', 'inputnode.epi')]),
# prepare field map
(selectfiles, topup_coreg, [('ap', 'inputnode.ap'),
('pa', 'inputnode.pa'),
('anat_head', 'inputnode.anat_head'),
('anat_brain', 'inputnode.anat_brain')
]),
(moco, topup_coreg, [('outputnode.epi_mean', 'inputnode.epi_mean')]),
# transform timeseries
(remove_vol, transform_ts, [('out_file', 'inputnode.orig_ts')]),
(selectfiles, transform_ts, [('anat_head', 'inputnode.anat_head')]),
(selectfiles, transform_ts, [('brain_mask', 'inputnode.brain_mask')]),
(moco, transform_ts, [('outputnode.mat_moco', 'inputnode.mat_moco')]),
(topup_coreg, transform_ts, [('outputnode.fmap_fullwarp', 'inputnode.fullwarp')]),
# correct slicetiming
# FIXME slice timing?
# (transform_ts, slicetiming, [('outputnode.trans_ts_masked', 'inputnode.ts')]),
# (slicetiming, denoise, [('outputnode.ts_slicetcorrected', 'inputnode.epi_coreg')]),
(transform_ts, denoise, [('outputnode.trans_ts_masked', 'inputnode.epi_coreg')]),
# denoise data
(selectfiles, denoise, [('brain_mask', 'inputnode.brain_mask'),
('anat_brain', 'inputnode.anat_brain')]),
(moco, denoise, [('outputnode.par_moco', 'inputnode.moco_par')]),
(topup_coreg, denoise, [('outputnode.epi2anat_dat', 'inputnode.epi2anat_dat'),
('outputnode.unwarped_mean_epi2fmap', 'inputnode.unwarped_mean')]),
(denoise, ants_registration, [('outputnode.normalized_file', 'inputnode.denoised_ts')]),
# registration to MNI space
(selectfiles, ants_registration, [('ants_affine', 'inputnode.ants_affine')]),
(selectfiles, ants_registration, [('ants_warp', 'inputnode.ants_warp')]),
# FL added fullspectrum
(denoise, ants_registration_full, [('outputnode.ts_fullspectrum', 'inputnode.denoised_ts')]),
(selectfiles, ants_registration_full, [('ants_affine', 'inputnode.ants_affine')]),
(selectfiles, ants_registration_full, [('ants_warp', 'inputnode.ants_warp')]),
(ants_registration, smoothing, [('outputnode.ants_reg_ts', 'inputnode.ts_transformed')]),
(smoothing, visualize, [('outputnode.ts_smoothed', 'inputnode.ts_transformed')]),
##all the output
(moco, sink, [ # ('outputnode.epi_moco', 'realign.@realigned_ts'),
('outputnode.par_moco', 'realign.@par'),
('outputnode.rms_moco', 'realign.@rms'),
('outputnode.mat_moco', 'realign.MAT.@mat'),
('outputnode.epi_mean', 'realign.@mean'),
('outputnode.rotplot', 'realign.plots.@rotplot'),
('outputnode.transplot', 'realign.plots.@transplot'),
('outputnode.dispplots', 'realign.plots.@dispplots'),
('outputnode.tsnr_file', 'realign.@tsnr')]),
(topup_coreg, sink, [('outputnode.fmap', 'coregister.transforms2anat.@fmap'),
# ('outputnode.unwarpfield_epi2fmap', 'coregister.@unwarpfield_epi2fmap'),
('outputnode.unwarped_mean_epi2fmap', 'coregister.@unwarped_mean_epi2fmap'),
('outputnode.epi2fmap', 'coregister.@epi2fmap'),
# ('outputnode.shiftmap', 'coregister.@shiftmap'),
('outputnode.fmap_fullwarp', 'coregister.transforms2anat.@fmap_fullwarp'),
('outputnode.epi2anat', 'coregister.@epi2anat'),
('outputnode.epi2anat_mat', 'coregister.transforms2anat.@epi2anat_mat'),
('outputnode.epi2anat_dat', 'coregister.transforms2anat.@epi2anat_dat'),
('outputnode.epi2anat_mincost', 'coregister.@epi2anat_mincost')
]),
(transform_ts, sink, [('outputnode.trans_ts_masked', 'coregister.@full_transform_ts'),
('outputnode.trans_ts_mean', 'coregister.@full_transform_mean'),
('outputnode.resamp_brain', 'coregister.@resamp_brain')]),
(denoise, sink, [
('outputnode.wmcsf_mask', 'denoise.mask.@wmcsf_masks'),
('outputnode.combined_motion', 'denoise.artefact.@combined_motion'),
('outputnode.outlier_files', 'denoise.artefact.@outlier'),
('outputnode.intensity_files', 'denoise.artefact.@intensity'),
('outputnode.outlier_stats', 'denoise.artefact.@outlierstats'),
('outputnode.outlier_plots', 'denoise.artefact.@outlierplots'),
('outputnode.mc_regressor', 'denoise.regress.@mc_regressor'),
('outputnode.comp_regressor', 'denoise.regress.@comp_regressor'),
('outputnode.mc_F', 'denoise.regress.@mc_F'),
('outputnode.mc_pF', 'denoise.regress.@mc_pF'),
('outputnode.comp_F', 'denoise.regress.@comp_F'),
('outputnode.comp_pF', 'denoise.regress.@comp_pF'),
('outputnode.brain_mask_resamp', 'denoise.mask.@brain_resamp'),
('outputnode.brain_mask2epi', 'denoise.mask.@brain_mask2epi'),
('outputnode.normalized_file', 'denoise.@normalized'),
# FL added fullspectrum
('outputnode.ts_fullspectrum', 'denoise.@ts_fullspectrum')
]),
(ants_registration, sink, [('outputnode.ants_reg_ts', 'ants.@antsnormalized')]),
(ants_registration_full, sink, [('outputnode.ants_reg_ts', 'ants.@antsnormalized_fullspectrum')]),
(smoothing, sink, [('outputnode.ts_smoothed', '@smoothed.FWHM6')]),
])
func_preproc.write_graph(dotfilename='func_preproc.dot', graph2use='colored', format='pdf', simple_form=True)
func_preproc.run(plugin='MultiProc')