Skip to content

Surface recon determinism #818

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
ClePol wants to merge 2 commits into
base: dev
Choose a base branch
from
Draft

Surface recon determinism #818

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
266d070
Make surface reconstruction deterministic
ClePol May 13, 2026
3ba6895
Fix surfaceRAS header check
ClePol May 21, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions recon_surf/recon-surf.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -714,7 +714,7 @@ for hemi in lh rh ; do

# Check if the surfaceRAS was correctly set and exit otherwise (sanity check in case nibabel changes their default header behaviour)
{
cmd="mris_info $outmesh | tr -s ' ' | grep -q 'vertex locs : surfaceRAS'"
cmd="mris_info $outmesh | awk '\$1 == \"vertex\" && \$2 == \"locs\" && \$3 == \":\" && \$4 == \"surfaceRAS\" { found = 1 } END { exit !found }'"
echo "echo \"$cmd\""
echo "$timecmd $cmd"
} | tee -a "$CMDF"
Expand Down Expand Up @@ -794,7 +794,7 @@ for hemi in lh rh ; do
echo "echo \"\""
} | tee -a "$CMDF"

cmd="recon-all -subject $subject -hemi $hemi -fix -no-isrunning -umask $(umask) $hiresflag $fsthreads"
cmd="env OMP_NUM_THREADS=1 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 recon-all -subject $subject -hemi $hemi -fix -no-isrunning -umask $(umask) $hiresflag -threads 1 -itkthreads 1"
RunIt "$cmd" "$LF" "$CMDF"

# fix the surfaces if they are corrupt
Expand Down
2 changes: 1 addition & 1 deletion recon_surf/spherically_project.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -145,7 +145,7 @@ def get_flipped_area(tria):
return area

fem = Solver(tria, lump=False, use_cholmod=use_cholmod)
evals, evecs = fem.eigs(k=4)
evals, evecs = fem.eigs(k=4, rng=0)

if debug:
data = dict()
Expand Down
14 changes: 12 additions & 2 deletions recon_surf/spherically_project_wrapper.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,20 @@ def setup_options():

if __name__ == "__main__":
import sys
from os import environ
opts = setup_options()

# The spectral projection is sensitive to tiny threaded BLAS/eigensolver
# differences, and those can be amplified by later topology correction.
for var in (
"OMP_NUM_THREADS",
"OPENBLAS_NUM_THREADS",
"MKL_NUM_THREADS",
"NUMEXPR_NUM_THREADS",
"VECLIB_MAXIMUM_THREADS",
):
environ[var] = "1"

# identify whether sksparse is installed (in which case we can use_cholmod in LaPy
try:
# ignore ruff F401 (unused import)
Expand All @@ -59,8 +71,6 @@ def setup_options():
has_sksparse = False
# First try to run standard spherical project
try:
from os import environ

from recon_surf.spherically_project import spherically_project_surface

source_surface = opts.sd / opts.subject / "surf" / f"{opts.hemi}.smoothwm.nofix"
Expand Down
Loading