コード例 #1
0
ファイル: connectogram.py プロジェクト: dgoyard/caps-clindmri
def bedpostx_diffusion_model(outdir, dwi, bval, bvec, nodif_brain_mask):
    """
    <unit>
        <output name="bedpostx_dir"    type="Directory" />

        <input name="outdir"           type="Directory" />
        <input name="dwi"              type="File"      />
        <input name="bval"             type="File"      />
        <input name="bvec"             type="File"      />
        <input name="nodif_brain_mask" type="File"      />
    </unit>
    """
    bedpostx_indir = os.path.join(outdir, "bedpostx")

    create_bedpostx_indir(bedpostx_indir, dwi, bval, bvec, nodif_brain_mask)
    bedpostx_dir = bedpostx(bedpostx_indir)[0]

    return bedpostx_dir
コード例 #2
0
about 5 hours of compute time. This routine need specific files that are
checked with the 'bedpostx_datacheck' command.
"""

# copy all necessary files in the same repertory for the bedpostx execution
bedpostx_indir = os.path.join(subjdir, "diffusion")
bedpostx_outdir = os.path.join(subjdir, "diffusion.bedpostX")
if not os.path.isdir(bedpostx_indir):
    os.mkdir(bedpostx_indir)
if len(os.listdir(bedpostx_outdir)) == 0:
    shutil.copy2(mask_file, bedpostx_indir)
    data_ext = ".".join(args.diffusion_file.split(".")[1:])
    shutil.copy2(args.diffusion_file, os.path.join(
                 bedpostx_indir, "data." + data_ext))
    shutil.copy2(args.bvecs_file, os.path.join(bedpostx_indir, "bvecs"))
    shutil.copy2(args.bvals_file, os.path.join(bedpostx_indir, "bvals"))
    if not bedpostx_datacheck(bedpostx_indir, shfile=args.fslconfig):
        raise IOError("'{0}' does not contain the data expected by "
                      "'bedpostx'.".format(bedpostx_indir))

    # execute bedpostx
    (bedpostx_outdir, merged_th, merged_ph,
     merged_f, mean_th, mean_ph,
     mean_f, dyads) = bedpostx(
        bedpostx_indir,
        shfile=args.fslconfig)
else:
    merged_files = glob.glob(os.path.join(bedpostx_outdir, "merged*"))
    if len(merged_files) == 0:
        raise IOError("FilesDoNotExist: in '{0}'.".format(bedpostx_outdir))
コード例 #3
0
if not os.path.isdir(bedpostx_indir):
    os.mkdir(bedpostx_indir)
if len(os.listdir(bedpostx_outdir)) == 0:
    shutil.copy2(mask_file, bedpostx_indir)
    data_ext = ".".join(diffusion_file.split(".")[1:])
    shutil.copy2(diffusion_file, os.path.join(bedpostx_indir,
                                              "data." + data_ext))
    shutil.copy2(bvecs_file, os.path.join(bedpostx_indir, "bvecs"))
    shutil.copy2(bvals_file, os.path.join(bedpostx_indir, "bvals"))
    if not bedpostx_datacheck(bedpostx_indir):
        raise IOError("'{0}' does not contain the data expected by "
                      "'bedpostx'.".format(bedpostx_indir))

    (bedpostx_outdir, merged_th, merged_ph,
     merged_f, mean_th, mean_ph,
     mean_f, dyads) = bedpostx(
        bedpostx_indir)
else:
    merged_files = glob.glob(os.path.join(bedpostx_outdir, "merged*"))
    if len(merged_files) == 0:
        raise IOError("FilesDoNotExist: in '{0}'.".format(bedpostx_outdir))

"""
Tractography
============

We compute the fibers starting at a specific gyrus, connecting the other
gyri only with the 'network' option. The result is stored in the 'fdt_paths'
image. The 'fdt_network_matrix' is a 2D region-by-region connectivity matrix.
"""

probtrackx2_outdir = os.path.join(outdir, "proba_region_connectivity")
コード例 #4
0
ファイル: fsl_bedpostx.py プロジェクト: dgoyard/caps-clindmri
# copy all necessary files in the same repertory for the bedpostx execution
bedpostx_indir = os.path.join(subjdir, "diffusion")
bedpostx_outdir = os.path.join(subjdir, "diffusion.bedpostX")
if not os.path.isdir(bedpostx_indir):
    os.mkdir(bedpostx_indir)
if not os.path.isdir(bedpostx_outdir) or len(os.listdir(bedpostx_outdir)) == 0:
    shutil.copy2(mask_file, bedpostx_indir)
    data_ext = ".".join(args.diffusion_file.split(".")[1:])
    shutil.copy2(args.diffusion_file, os.path.join(bedpostx_indir, "data." + data_ext))
    shutil.copy2(args.bvecs_file, os.path.join(bedpostx_indir, "bvecs"))
    shutil.copy2(args.bvals_file, os.path.join(bedpostx_indir, "bvals"))
    if not bedpostx_datacheck(bedpostx_indir, shfile=args.fslconfig):
        raise IOError("'{0}' does not contain the data expected by " "'bedpostx'.".format(bedpostx_indir))

    # execute bedpostx
    if not args.rician:
        args.rician = None
    (bedpostx_outdir, merged_th, merged_ph, merged_f, mean_th, mean_ph, mean_f, mean_d, mean_S0, dyads) = bedpostx(
        bedpostx_indir,
        n=args.n,
        model=args.model,
        rician=args.rician,
        shfile=args.fslconfig,
        b=args.burnin,
        cpus=args.cpus,
    )
else:
    merged_files = glob.glob(os.path.join(bedpostx_outdir, "merged*"))
    if len(merged_files) == 0:
        raise IOError("FilesDoNotExist: in '{0}'.".format(bedpostx_outdir))
コード例 #5
0
bedpostx_indir = os.path.join(subjdir, "diffusion")
bedpostx_outdir = os.path.join(subjdir, "diffusion.bedpostX")
if not os.path.isdir(bedpostx_indir):
    os.mkdir(bedpostx_indir)
if not os.path.isdir(bedpostx_outdir) or len(os.listdir(bedpostx_outdir)) == 0:
    shutil.copy2(mask_file, bedpostx_indir)
    data_ext = ".".join(args.diffusion_file.split(".")[1:])
    shutil.copy2(args.diffusion_file,
                 os.path.join(bedpostx_indir, "data." + data_ext))
    shutil.copy2(args.bvecs_file, os.path.join(bedpostx_indir, "bvecs"))
    shutil.copy2(args.bvals_file, os.path.join(bedpostx_indir, "bvals"))
    if not bedpostx_datacheck(bedpostx_indir, shfile=args.fslconfig):
        raise IOError("'{0}' does not contain the data expected by "
                      "'bedpostx'.".format(bedpostx_indir))

    # execute bedpostx
    if not args.rician:
        args.rician = None
    (bedpostx_outdir, merged_th, merged_ph, merged_f, mean_th, mean_ph, mean_f,
     mean_d, mean_S0, dyads) = bedpostx(bedpostx_indir,
                                        n=args.n,
                                        model=args.model,
                                        rician=args.rician,
                                        shfile=args.fslconfig,
                                        b=args.burnin,
                                        cpus=args.cpus)
else:
    merged_files = glob.glob(os.path.join(bedpostx_outdir, "merged*"))
    if len(merged_files) == 0:
        raise IOError("FilesDoNotExist: in '{0}'.".format(bedpostx_outdir))
コード例 #6
0
ファイル: fsl_bedpostx.py プロジェクト: gareaut/caps-clindmri
checked with the 'bedpostx_datacheck' command.
"""

# copy all necessary files in the same repertory for the bedpostx execution
bedpostx_indir = os.path.join(subjdir, "diffusion")
bedpostx_outdir = os.path.join(subjdir, "diffusion.bedpostX")
if not os.path.isdir(bedpostx_indir):
    os.mkdir(bedpostx_indir)
if not os.path.isdir(bedpostx_outdir) or len(os.listdir(bedpostx_outdir)) == 0:
    shutil.copy2(mask_file, bedpostx_indir)
    data_ext = ".".join(args.diffusion_file.split(".")[1:])
    shutil.copy2(args.diffusion_file, os.path.join(
                 bedpostx_indir, "data." + data_ext))
    shutil.copy2(args.bvecs_file, os.path.join(bedpostx_indir, "bvecs"))
    shutil.copy2(args.bvals_file, os.path.join(bedpostx_indir, "bvals"))
    if not bedpostx_datacheck(bedpostx_indir, shfile=args.fslconfig):
        raise IOError("'{0}' does not contain the data expected by "
                      "'bedpostx'.".format(bedpostx_indir))

    # execute bedpostx
    if not args.rician:
        args.rician = None
    (bedpostx_outdir, merged_th, merged_ph, merged_f, mean_th, mean_ph, mean_f,
     mean_d, mean_S0, dyads) = bedpostx(
        bedpostx_indir, n=args.n, model=args.model, rician=args.rician,
        shfile=args.fslconfig, b=args.burnin, cpus=args.cpus)
else:
    merged_files = glob.glob(os.path.join(bedpostx_outdir, "merged*"))
    if len(merged_files) == 0:
        raise IOError("FilesDoNotExist: in '{0}'.".format(bedpostx_outdir))