def rs_grouplevel(z, prefix, output_dir, work_dir):
from nipype.interfaces.fsl.model import Randomise
from nipype.interfaces import fsl as fsl
merger = fsl.utils.Merge()
merger.inputs.in_files = z
merger.inputs.dimension = 't'
merger.inputs.merged_file = op.join(work_dir, 'z_merge.nii.gz')
merger.run()
immaths = fsl.utils.ImageMaths()
immaths.inputs.in_file = op.join(work_dir, 'z_merge.nii.gz')
immaths.inputs.op_string = "-abs -bin -Tmin"
immaths.inputs.out_file = op.join(work_dir, 'mask.nii.gz')
immaths.run()
masker = fsl.maths.ApplyMask()
masker.inputs.in_file = op.join(work_dir, 'z_merge.nii.gz')
masker.inputs.mask_file = op.join(work_dir, 'mask.nii.gz')
masker.inputs.out_file = op.join(work_dir, 'z_merge.nii.gz')
masker.run()
meaner = fsl.utils.ImageMaths()
meaner.inputs.in_file = op.join(work_dir, 'z_merge.nii.gz')
meaner.inputs.op_string = "-Tmean"
meaner.inputs.out_file = op.join(work_dir, 'z.nii.gz')
meaner.run()
shutil.copyfile(op.join(work_dir, 'z.nii.gz'), op.join(output_dir, '{prefix}_z.nii.gz'.format(prefix=prefix)))
randomise = Randomise()
randomise.inputs.in_file = op.join(work_dir, 'z_merge.nii.gz')
randomise.inputs.mask = op.join(work_dir, 'mask.nii.gz')
randomise.inputs.one_sample_group_mean = True
randomise.inputs.raw_stats_imgs = True
randomise.inputs.vox_p_values = True
randomise.inputs.base_name = 'randomise'
os.chdir(work_dir)
randomise.run()
thresher = fsl.utils.ImageMaths()
thresher.inputs.in_file = op.join(work_dir, 'randomise_vox_corrp_tstat1.nii.gz')
thresher.inputs.op_string = "-thr 0.999"
thresher.inputs.out_file = op.join(work_dir, 'randomise_vox_corrp_tstat1_thr001.nii.gz')
thresher.run()
masker = fsl.maths.ApplyMask()
masker.inputs.in_file = op.join(work_dir, 'randomise_tstat1.nii.gz')
masker.inputs.mask_file = op.join(work_dir, 'randomise_vox_corrp_tstat1_thr001.nii.gz')
masker.inputs.out_file = op.join(work_dir, 'randomise_tstat1_thr001.nii.gz')
masker.run()
#copy data to directory vox_corrp_tstat1.nii.gz
shutil.copyfile(op.join(work_dir, 'randomise_tstat1.nii.gz'), op.join(output_dir, '{prefix}_tstat1.nii.gz'.format(prefix=prefix)))
shutil.copyfile(op.join(work_dir, 'randomise_vox_corrp_tstat1.nii.gz'), op.join(output_dir, '{prefix}_vox_corrp.nii.gz'.format(prefix=prefix)))
shutil.copyfile(op.join(work_dir, 'randomise_tstat1_thr001.nii.gz'), op.join(output_dir, '{prefix}_tstat1_thr001.nii.gz'.format(prefix=prefix)))
shutil.rmtree(work_dir)
