From bdc027722a282e7ae7a60e84bc004cc9f4f310d3 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 1/4] Make surface reconstruction deterministic

---
 recon_surf/recon-surf.sh                  |  2 +-
 recon_surf/spherically_project_wrapper.py | 14 ++++++++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/recon_surf/recon-surf.sh b/recon_surf/recon-surf.sh
index 8bfca5a82..4d1d648d7 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_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 cc66fddc89cfaab7135b9e7fa9fb546680f3d5dc Mon Sep 17 00:00:00 2001
From: Clemens Pollak <ClePol@users.noreply.github.com>
Date: Mon, 29 Jun 2026 18:15:45 +0200
Subject: [PATCH 2/4] Update recon_surf/recon-surf.sh

Co-authored-by: Martin Reuter <m-reuter@users.noreply.github.com>
---
 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 4d1d648d7..4da4cc97b 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="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"
+    cmd="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

From b93744b7d6440893174cbdfe9d0f564e24ac1999 Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Wed, 1 Jul 2026 15:40:37 +0200
Subject: [PATCH 3/4] fixing to 1 thread here does not seem to be needed in my
 experiments on linux and mac

---
 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 4da4cc97b..8bfca5a82 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 -threads 1 -itkthreads 1"
+    cmd="recon-all -subject $subject -hemi $hemi -fix -no-isrunning -umask $(umask) $hiresflag $fsthreads"
     RunIt "$cmd" "$LF" "$CMDF"
 
     # fix the surfaces if they are corrupt

From 025dbbd02510558d83ee73bb3e58a028e000ebec Mon Sep 17 00:00:00 2001
From: Martin Reuter <m-reuter@users.noreply.github.com>
Date: Wed, 1 Jul 2026 15:41:26 +0200
Subject: [PATCH 4/4] numexpr is not a dependency here

---
 recon_surf/spherically_project_wrapper.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/recon_surf/spherically_project_wrapper.py b/recon_surf/spherically_project_wrapper.py
index 957c2a06e..fca12566c 100644
--- a/recon_surf/spherically_project_wrapper.py
+++ b/recon_surf/spherically_project_wrapper.py
@@ -57,7 +57,6 @@ def setup_options():
         "OMP_NUM_THREADS",
         "OPENBLAS_NUM_THREADS",
         "MKL_NUM_THREADS",
-        "NUMEXPR_NUM_THREADS",
         "VECLIB_MAXIMUM_THREADS",
     ):
         environ[var] = "1"