reslice = Node(MRIConvert(vox_size=resampled_voxel_size, out_type='nii'),
name='reslice')
# Segment structural scan
#segment = Node(Segment(affine_regularization='none'), name='segment')
segment = Node(FAST(no_bias=True, segments=True, number_classes=3),
name='segment')
#Slice timing correction based on interleaved acquisition using FSL
slicetime_correct = Node(SliceTimer(interleaved=interleave,
slice_direction=slice_dir,
time_repetition=TR),
name='slicetime_correct')
# Motion correction
motion_correct = Node(MCFLIRT(save_plots=True, mean_vol=True),
name='motion_correct')
# Registration- using FLIRT
# The BOLD image is 'in_file', the anat is 'reference', the output is 'out_file'
coreg1 = Node(FLIRT(), name='coreg1')
coreg2 = Node(FLIRT(apply_xfm=True), name='coreg2')
# make binary mask
# structural is the 'in_file', output is 'binary_file'
binarize_struct = Node(Binarize(dilate=mask_dilation,
erode=mask_erosion,
min=1),
name='binarize_struct')
# apply the binary mask to the functional data
