def get_volume(mask, thresh, out_file):
Mask = MathsCommand(in_file = mask,
args = "-thr {0} -bin".format(thresh),
out_file=out_file)
Mout = Mask.run()
Volume = ImageStats(in_file = mask, op_string = '-l {0} -V'.format(thresh))
Vout=Volume.run()
outstat = Vout.outputs.out_stat
return outstat[1]
# get group level probabilistic GM by averaging maths = MultiImageMaths() maths.inputs.in_file = gm_list[0] maths.inputs.op_string = op_string_gm maths.inputs.operand_files = gm_list[1:] maths.inputs.out_file = 'gm_prob_mni3_ave.nii.gz' maths.run() #print maths.cmdline # get GM mask (binarize the probabilistic GM map) binarize = MathsCommand() binarize.inputs.args = '-thr 0.30 -bin' binarize.inputs.in_file = 'gm_prob_mni3_ave.nii.gz' binarize.inputs.out_file = 'gm_prob_mni3_ave_mask.nii.gz' binarize.run() # get group level resting mask by multiplying individual ones maths = MultiImageMaths() maths.inputs.in_file = rest_list[0] maths.inputs.op_string = op_string_rest maths.inputs.operand_files = rest_list[1:] maths.inputs.out_file = 'rest_mask_mni3_ave.nii.gz' maths.run() ############# Step 2 ####################################### maths = MultiImageMaths() maths.inputs.in_file = 'gm_prob_mni3_ave_mask.nii.gz' maths.inputs.op_string = '-mul %s' maths.inputs.operand_files = 'rest_mask_mni3_ave.nii.gz' maths.inputs.out_file = 'mni3_rest_gm_mask.nii.gz'
