Mercurial > repos > greg > drmi
changeset 18:f15d37b5efea draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 03 Nov 2017 14:45:44 -0400 |
| parents | 947059a3876d |
| children | 3938c3299e7b |
| files | dmri.py |
| diffstat | 1 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/dmri.py Fri Nov 03 14:45:38 2017 -0400 +++ b/dmri.py Fri Nov 03 14:45:44 2017 -0400 @@ -11,7 +11,7 @@ parser = argparse.ArgumentParser() parser.add_argument('--input', dest='input', help='Input dataset') -parser.add_argument('--output_gtab', dest='output_gtab', help='Output gradient table dataset') +parser.add_argument('--output_nifti1', dest='output_nifti1', help='Output Nifti1 dataset') parser.add_argument('--output_png', dest='output_png', help='Output dataset') args = parser.parse_args() @@ -40,5 +40,9 @@ # Load the b-values and b-vectors. bvals, bvecs = read_bvals_bvecs(fbval, fbvec) gtab = gradient_table(bvals, bvecs) -with open(args.output_gtab, 'w') as fh: - fh.write(gtab.info) \ No newline at end of file +# gtab can be used to tell what part of the data is the S0 +# volumes (volumes which correspond to b-values of 0). +S0s = data[:, :, :, gtab.b0s_mask] +# Save this in a new Nifti file. +nib.save(nib.Nifti1Image(S0s, img.affine), 'HARDI193_S0.nii') +shutil.move('HARDI193_S0.nii', args.output_nifti1)