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Merged
merged 3 commits into from
Nov 14, 2025
Merged

[ENH] Add more info for noddi priors #1278

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1172574
add more info for noddi priors
arnaudbore Nov 13, 2025
d59c11d
add header
arnaudbore Nov 13, 2025
e0f1e9f
temporary change the way vtk-osmesa is installed
arnaudbore Nov 14, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/test-ml.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ jobs:
# TODO: to adapt once Scilpy passes to VTK 9.4.0, which selects OSMesa at runtime
# https://discourse.vtk.org/t/status-update-runtime-opengl-render-window-selection-in-vtk/14583
VTK_VERSION=$(cat pyproject.toml | grep 'vtk==' | sed 's/vtk==//g' | sed 's/\"//g' )
uv pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
uv pip install pytest-xdist pytest-cov
uv pip install torch==2.2.1 torchvision==0.17.1

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2 changes: 1 addition & 1 deletion .github/workflows/test.yml
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Expand Up @@ -67,7 +67,7 @@ jobs:
# TODO: to adapt once Scilpy passes to VTK 9.4.0, which selects OSMesa at runtime
# https://discourse.vtk.org/t/status-update-runtime-opengl-render-window-selection-in-vtk/14583
VTK_VERSION=$(cat pyproject.toml | grep 'vtk==' | sed 's/vtk==//g' | sed 's/\"//g' )
uv pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
uv pip install pytest-xdist pytest-cov
scil_data_download
scil_search_keywords test --regenerate_help_files --processes 8
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2 changes: 1 addition & 1 deletion .github/workflows/test_tutorials.yml
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Expand Up @@ -66,7 +66,7 @@ jobs:
# TODO: to adapt once Scilpy passes to VTK 9.4.0, which selects OSMesa at runtime
# https://discourse.vtk.org/t/status-update-runtime-opengl-render-window-selection-in-vtk/14583
VTK_VERSION=$(cat pyproject.toml | grep 'vtk==' | sed 's/vtk==//g' | sed 's/\"//g' )
uv pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
uv pip install pytest-xdist pytest-cov
uv pip install gdown

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31 changes: 26 additions & 5 deletions src/scilpy/cli/scil_NODDI_priors.py
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Expand Up @@ -150,8 +150,12 @@ def main():
.format(args.fa_min_single_fiber, 0.95, nb_voxels))
single_fiber_ad_mean = np.mean(roi_ad[indices])
single_fiber_ad_std = np.std(roi_ad[indices])
single_fiber_ad_max = np.max(roi_ad[indices])
single_fiber_ad_min = np.min(roi_ad[indices])
single_fiber_rd_mean = np.mean(roi_rd[indices])
single_fiber_rd_std = np.std(roi_rd[indices])
single_fiber_rd_max = np.max(roi_rd[indices])
single_fiber_rd_min = np.min(roi_rd[indices])

# Create mask of single fiber in ROI
indices[0][:] += ci - w
Expand All @@ -168,7 +172,9 @@ def main():
'{}'.format(args.fa_max_ventricles, args.md_min_ventricles,
nb_voxels))

vent_avg = np.mean(roi_md[indices])
vent_mean = np.mean(roi_md[indices])
vent_min = np.min(roi_md[indices])
vent_max = np.max(roi_md[indices])
vent_std = np.std(roi_md[indices])

# Create mask of ventricle in ROI
Expand All @@ -187,20 +193,35 @@ def main():
nib.save(nib.Nifti1Image(mask_vent, affine), args.out_mask_ventricles)

if args.out_txt_1fiber_para:
np.savetxt(args.out_txt_1fiber_para, [single_fiber_ad_mean], fmt='%f')
single_fiber_ad = np.array([single_fiber_ad_mean,
single_fiber_ad_std,
single_fiber_ad_min,
single_fiber_ad_max])[np.newaxis, :]
np.savetxt(args.out_txt_1fiber_para, single_fiber_ad,
header="mean std min max", fmt='%f')

if args.out_txt_1fiber_perp:
np.savetxt(args.out_txt_1fiber_perp, [single_fiber_rd_mean], fmt='%f')
single_fiber_rd = np.array([single_fiber_rd_mean,
single_fiber_rd_std,
single_fiber_rd_min,
single_fiber_rd_max])[np.newaxis, :]
np.savetxt(args.out_txt_1fiber_perp, single_fiber_rd,
header="mean std min max", fmt='%f')

if args.out_txt_ventricles:
np.savetxt(args.out_txt_ventricles, [vent_avg], fmt='%f')
vent = np.array([vent_mean,
vent_std,
vent_min,
vent_max])[np.newaxis, :]
np.savetxt(args.out_txt_ventricles, vent,
header="mean std min max", fmt='%f')

logging.info("Average AD in single fiber areas: {} +- {}"
.format(single_fiber_ad_mean, single_fiber_ad_std))
logging.info("Average RD in single fiber areas: {} +- {}"
.format(single_fiber_rd_mean, single_fiber_rd_std))
logging.info("Average MD in ventricles: {} +- {}"
.format(vent_avg, vent_std))
.format(vent_mean, vent_std))


if __name__ == "__main__":
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