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Add perpendicular diffusivity in NODDI priors #872

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merged 4 commits into from
Feb 14, 2024
Merged

Add perpendicular diffusivity in NODDI priors #872

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b89caae
add perp_diff to priors
gagnonanthony Dec 6, 2023
78f53e6
Merge branch 'origin/master' into perpdiff
gagnonanthony Dec 19, 2023
a5f67a7
update test + pep8
gagnonanthony Dec 19, 2023
6f0d51c
Merge branch 'upstream/master' into perpdiff
gagnonanthony Feb 14, 2024
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45 changes: 34 additions & 11 deletions scripts/scil_NODDI_priors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,8 @@
# -*- coding: utf-8 -*-

"""
Compute the axial (para_diff) and mean (iso_diff) diffusivity priors for NODDI.
Compute the axial (para_diff), radial (perp_diff),
and mean (iso_diff) diffusivity priors for NODDI.

Formerly: scil_compute_NODDI_priors.py
"""
Expand Down Expand Up @@ -37,6 +38,8 @@ def _build_arg_parser():
help='Path to the FA volume.')
p.add_argument('in_AD',
help='Path to the axial diffusivity (AD) volume.')
p.add_argument('in_RD',
help='Path to the radial diffusivity (RD) volume.')
p.add_argument('in_MD',
help='Path to the mean diffusivity (MD) volume.')

Expand Down Expand Up @@ -66,10 +69,14 @@ def _build_arg_parser():
'priors. [center of the 3D volume]')

g3 = p.add_argument_group('Outputs')
g3.add_argument('--out_txt_1fiber', metavar='FILE',
g3.add_argument('--out_txt_1fiber_para', metavar='FILE',
help='Output path for the text file containing the single '
'fiber average value of AD.\nIf not set, the file '
'will not be saved.')
g3.add_argument('--out_txt_1fiber_perp', metavar='FILE',
help='Output path for the text file containing the single '
'fiber average value of RD.\nIf not set, the file '
'will not be saved.')
g3.add_argument('--out_mask_1fiber', metavar='FILE',
help='Output path for single fiber mask. If not set, the '
'mask will not be saved.')
Expand All @@ -91,14 +98,16 @@ def main():
parser = _build_arg_parser()
args = parser.parse_args()

assert_inputs_exist(parser, [args.in_AD, args.in_FA, args.in_MD])
assert_inputs_exist(parser, [args.in_AD, args.in_FA, args.in_MD,
args.in_RD])
assert_outputs_exist(parser, args, [],
[args.out_mask_1fiber,
args.out_mask_ventricles,
args.out_txt_ventricles,
args.out_txt_1fiber])
args.out_txt_1fiber_para,
args.out_txt_1fiber_perp])

assert_same_resolution([args.in_AD, args.in_FA, args.in_MD])
assert_same_resolution([args.in_AD, args.in_FA, args.in_MD, args.in_RD])

log_level = logging.DEBUG if args.verbose else logging.INFO
logging.getLogger().setLevel(log_level)
Expand All @@ -109,6 +118,7 @@ def main():

md_data = nib.load(args.in_MD).get_fdata(dtype=np.float32)
ad_data = nib.load(args.in_AD).get_fdata(dtype=np.float32)
rd_data = nib.load(args.in_RD).get_fdata(dtype=np.float32)

mask_cc = np.zeros(fa_data.shape, dtype=np.uint8)
mask_vent = np.zeros(fa_data.shape, dtype=np.uint8)
Expand All @@ -129,6 +139,9 @@ def main():
roi_ad = ad_data[max(int(ci - w), 0): min(int(ci + w), fa_shape[0]),
max(int(cj - w), 0): min(int(cj + w), fa_shape[1]),
max(int(ck - w), 0): min(int(ck + w), fa_shape[2])]
roi_rd = rd_data[max(int(ci - w), 0): min(int(ci + w), fa_shape[0]),
max(int(cj - w), 0): min(int(cj + w), fa_shape[1]),
max(int(ck - w), 0): min(int(ck + w), fa_shape[2])]
roi_md = md_data[max(int(ci - w), 0): min(int(ci + w), fa_shape[0]),
max(int(cj - w), 0): min(int(cj + w), fa_shape[1]),
max(int(ck - w), 0): min(int(ck + w), fa_shape[2])]
Expand All @@ -144,8 +157,11 @@ def main():

logging.debug('Number of voxels found in single fiber area: {}'.format(N))

cc_avg = np.mean(roi_ad[indices])
cc_std = np.std(roi_ad[indices])
cc_avg_para = np.mean(roi_ad[indices])
cc_std_para = np.std(roi_ad[indices])

cc_avg_perp = np.mean(roi_rd[indices])
cc_std_perp = np.std(roi_rd[indices])

indices[0][:] += ci - w
indices[1][:] += cj - w
Expand All @@ -171,14 +187,21 @@ def main():
if args.out_mask_ventricles:
nib.save(nib.Nifti1Image(mask_vent, affine), args.out_mask_ventricles)

if args.out_txt_1fiber:
np.savetxt(args.out_txt_1fiber, [cc_avg], fmt='%f')
if args.out_txt_1fiber_para:
np.savetxt(args.out_txt_1fiber_para, [cc_avg_para], fmt='%f')

if args.out_txt_1fiber_perp:
np.savetxt(args.out_txt_1fiber_perp, [cc_avg_perp], fmt='%f')

if args.out_txt_ventricles:
np.savetxt(args.out_txt_ventricles, [vent_avg], fmt='%f')

logging.info("Average AD in single fiber areas: {} +- {}".format(cc_avg,
cc_std))
logging.info("Average AD in single fiber areas: {} +- {}".format(
cc_avg_para,
cc_std_para))
logging.info("Average RD in single fiber areas: {} +- {}".format(
cc_avg_perp,
cc_std_perp))
logging.info("Average MD in ventricles: {} +- {}".format(vent_avg,
vent_std))

Expand Down
15 changes: 9 additions & 6 deletions scripts/tests/test_NODDI_priors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
from scilpy.io.fetcher import fetch_data, get_home, get_testing_files_dict

# If they already exist, this only takes 5 seconds (check md5sum)
fetch_data(get_testing_files_dict(), keys=['commit_amico.zip'])
fetch_data(get_testing_files_dict(), keys=['processing.zip'])
tmp_dir = tempfile.TemporaryDirectory()


Expand All @@ -18,14 +18,17 @@ def test_help_option(script_runner):

def test_execution_commit_amico(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_fa = os.path.join(get_home(), 'commit_amico',
in_fa = os.path.join(get_home(), 'processing',
'fa.nii.gz')
in_ad = os.path.join(get_home(), 'commit_amico',
in_ad = os.path.join(get_home(), 'processing',
'ad.nii.gz')
in_md = os.path.join(get_home(), 'commit_amico',
in_md = os.path.join(get_home(), 'processing',
'md.nii.gz')
ret = script_runner.run('scil_NODDI_priors.py', in_fa, in_ad, in_md,
'--out_txt_1fiber', '1fiber.txt',
in_rd = os.path.join(get_home(), 'processing',
'rd.nii.gz')
ret = script_runner.run('scil_NODDI_priors.py', in_fa, in_ad, in_rd, in_md,
'--out_txt_1fiber_para', '1fiber_para.txt',
'--out_txt_1fiber_perp', '1fiber_perp.txt',
'--out_mask_1fiber', '1fiber.nii.gz',
'--out_txt_ventricles', 'ventricules.txt',
'--out_mask_ventricles', 'ventricules.nii.gz')
Expand Down
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