891e580bc8e66d0d81c2334c507cd1b10f93cbc2,pynets/utils.py,,reorient_dwi,#Any#Any#Any#,897

Before Change

    import shutil
    // Check orientation (dwi_prep)
    cmd = "fslorient -getorient " + dwi_prep
    orient = os.popen(cmd).read().strip("\n")
    dwi_orig = dwi_prep
    dwi_prep = "{}/{}_pre_reor.nii.gz".format(out_dir, dwi_prep.split("/")[-1].split(".nii.gz")[0])
    shutil.copyfile(dwi_orig, dwi_prep)
    bvecs_orig = bvecs

After Change

    import shutil
    // Check orientation (dwi_prep)
    cmd = "fslorient -getorient " + dwi_prep
    cmd_run = os.popen(cmd)
    orient = cmd_run.read().strip("\n")
    cmd_run.close()
    dwi_orig = dwi_prep
    dwi_prep = "{}/{}_pre_reor.nii.gz".format(out_dir, dwi_prep.split("/")[-1].split(".nii.gz")[0])
    shutil.copyfile(dwi_orig, dwi_prep)
    bvecs_orig = bvecs
    bvecs = "{}/bvecs.bvec".format(out_dir)
    shutil.copyfile(bvecs_orig, bvecs)
    bvecs_mat = np.genfromtxt(bvecs)
    cmd = "fslorient -getqform " + dwi_prep
    cmd_run = os.popen(cmd)
    qform = cmd_run.read().strip("\n")
    cmd_run.close()
    reoriented = False
    if orient == "NEUROLOGICAL":
        reoriented = True
        print("Neurological (dwi), reorienting to radiological...")
        // Orient dwi to RADIOLOGICAL
        // Posterior-Anterior Reorientation
        if float(qform.split(" ")[:-1][5]) <= 0:
            dwi_prep_PA = "{}/dwi_reor_PA.nii.gz".format(out_dir)
            print("Reorienting P-A flip (dwi)...")
            cmd = "fslswapdim " + dwi_prep + " -x -y z " + dwi_prep_PA
            os.system(cmd)
            bvecs_mat[:,1] = -bvecs_mat[:,1]
            cmd = "fslorient -getqform " + dwi_prep_PA
            cmd_run = os.popen(cmd)
            qform = cmd_run.read().strip("\n")
            cmd_run.close()
            dwi_prep = dwi_prep_PA
        // Inferior-Superior Reorientation
        if float(qform.split(" ")[:-1][10]) <= 0:

Instances