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
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))
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")
# 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))
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))
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))