aligned-mri/code/calc_tsnr

#!/usr/bin/python
"""
Compute a tSNR volume given an input time series image.
"""

import os
import sys

if not len(sys.argv) == 2:
    print __doc__
    sys.exit(1)

import nibabel as nb
from mvpa2.mappers.detrend import poly_detrend
from mvpa2.datasets.mri import fmri_dataset
from mvpa2.datasets.mri import map2nifti

infilename = sys.argv[1]
outfilename = os.path.splitext(infilename)[0]
if outfilename.endswith('.nii'):
    outfilename = os.path.splitext(outfilename)[0]
outfilename += '_tsnr.nii.gz'

ds = fmri_dataset(infilename)
# clip the value range, can only be negative due to interpolation
# regime
ds.samples[ds.samples < 0] = 0
# first capture mean -- detrending will bring it close to zero
m = ds.samples.mean(axis=0)
# now detrend
poly_detrend(ds, polyord=1)
# and get the std after linear trend removal
std = ds.samples.std(axis=0)
# compute tSNR
m[std > 0] /= std[std > 0]
# protect against ultra-low noise voxels (images are zero'ed at the edges)
m[m > 1000] = 1000

map2nifti(ds, m).to_filename(outfilename)