From 266d070f2cd8779ba4c244cfd6a072ce146d2f6a Mon Sep 17 00:00:00 2001
From: ClePol <ClePol@users.noreply.github.com>
Date: Wed, 13 May 2026 15:45:36 +0200
Subject: [PATCH 1/2] Make surface reconstruction deterministic

---
 recon_surf/recon-surf.sh                  |  2 +-
 recon_surf/spherically_project.py         |  2 +-
 recon_surf/spherically_project_wrapper.py | 14 ++++++++++++--
 3 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/recon_surf/recon-surf.sh b/recon_surf/recon-surf.sh
index e0e480493..eac769aef 100755
--- a/recon_surf/recon-surf.sh
+++ b/recon_surf/recon-surf.sh
@@ -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
diff --git a/recon_surf/spherically_project.py b/recon_surf/spherically_project.py
index c0706d47a..0de5c4649 100644
--- a/recon_surf/spherically_project.py
+++ b/recon_surf/spherically_project.py
@@ -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()
diff --git a/recon_surf/spherically_project_wrapper.py b/recon_surf/spherically_project_wrapper.py
index 09b3eb9bd..957c2a06e 100644
--- a/recon_surf/spherically_project_wrapper.py
+++ b/recon_surf/spherically_project_wrapper.py
@@ -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)
@@ -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"

From 3ba6895e7289b7763d05a991ea84b159a4b3b45f Mon Sep 17 00:00:00 2001
From: ClePol <ClePol@users.noreply.github.com>
Date: Thu, 21 May 2026 12:05:57 +0200
Subject: [PATCH 2/2] Fix surfaceRAS header check

---
 recon_surf/recon-surf.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/recon_surf/recon-surf.sh b/recon_surf/recon-surf.sh
index eac769aef..4d1d648d7 100755
--- a/recon_surf/recon-surf.sh
+++ b/recon_surf/recon-surf.sh
@@ -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"