d64b3e882f106f19ea02a5a6066e60a9c0616c5b,pynets/core/utils.py,,make_gtab_and_bmask,#Any#Any#Any#Any#Any#Any#,1413

Before Change

    // Extract and Combine all b0s collected
    print("Extracting b0\"s...")
    cmds = []
    b0s_bbr = []
    for b0 in b0s:
        print(b0)
        b0_bbr = "{}/{}_b0.nii.gz".format(namer_dir, str(b0))
        cmds.append("fslroi {} {} {} 1".format(dwi_file, b0_bbr, str(b0), " 1"))
        b0s_bbr.append(b0_bbr)

    for cmd in cmds:
        os.system(cmd)

    // Get mean b0
    mean_b0 = mean_img(b0s_bbr)
    nib.save(mean_b0, B0)

    // Get mean b0 brain mask

After Change

        b0_vols.append(dwi_data[:, :, :, b0])

    // Save mean B0
    mean_B0_img = mean_img([nib.Nifti1Image(B0, affine=dwi_img.affine) for B0 in b0_vols])
    nib.save(mean_B0_img, B0)

    // Create mean b0 brain mask
    mean_b0_mask = compute_epi_mask(mean_B0_img, lower_cutoff=0.15, upper_cutoff=0.75)

Instances