import sys from nipype.interfaces import afni from nipype.interfaces.fsl.maths import BinaryMaths ### despikes fMRI timeseries for subjects with > 1mm motion peak # inputname = 'sub-05_ses-03_task-future_bold_space-MNI152NLin2009cAsym_preproc.nii.gz' inputname = sys.argv[1] outputname = inputname[:-7] + '_despiked.nii.gz' # afni 3dDespike despike = afni.Despike() despike.inputs.in_file = inputname despike.inputs.out_file = outputname despike.inputs.args = '-cut 1.0 4.0' print(despike.cmdline) despike.run() # subtract despiked image from the original to check the diff subtract = BinaryMaths() subtract.inputs.in_file = inputname subtract.inputs.operand_file = outputname subtract.inputs.operation = 'sub' subtract.inputs.out_file = outputname[:-7] + '_diff.nii.gz' print(subtract.cmdline) subtract.run()
