From 8794ec2613466eddd29749987c014c4b1c373ab3 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 6 Sep 2023 13:03:15 -0400
Subject: [PATCH 1/3] MNT: Add sloppy MSM config

---
 smriprep/data/msm/MSMSulcStrainSloppyconf | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 smriprep/data/msm/MSMSulcStrainSloppyconf

diff --git a/smriprep/data/msm/MSMSulcStrainSloppyconf b/smriprep/data/msm/MSMSulcStrainSloppyconf
new file mode 100644
index 0000000000..4d612fe7a6
--- /dev/null
+++ b/smriprep/data/msm/MSMSulcStrainSloppyconf
@@ -0,0 +1,18 @@
+--simval=3,2
+--sigma_in=0,0
+--sigma_ref=0,0
+--lambda=0,10
+--it=20,5
+--opt=AFFINE,DISCRETE
+--CPgrid=6,2
+--SGgrid=6,4
+--datagrid=6,4
+--regoption=3
+--regexp=2
+--dopt=HOCR
+--VN
+--rescaleL
+--triclique
+--k_exponent=2
+--bulkmod=1.6
+--shearmod=0.4

From 39a0e2374546a9ae8825baf6c086bb6edbb3978c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 6 Sep 2023 13:07:09 -0400
Subject: [PATCH 2/3] ENH: Pass sloppy parameter to MSM workflow to select
 cheaper config

---
 smriprep/workflows/anatomical.py |  2 +-
 smriprep/workflows/surfaces.py   | 14 ++++++++++----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
index 6187044895..738ec03941 100644
--- a/smriprep/workflows/anatomical.py
+++ b/smriprep/workflows/anatomical.py
@@ -530,7 +530,7 @@ def _check_img(img):
         name="surface_recon_wf", omp_nthreads=omp_nthreads, hires=hires
     )
     applyrefined = pe.Node(fsl.ApplyMask(), name="applyrefined")
-    sphere_reg_wf = init_sphere_reg_wf(msm_sulc=msm_sulc, name="sphere_reg_wf")
+    sphere_reg_wf = init_sphere_reg_wf(msm_sulc=msm_sulc, sloppy=sloppy, name="sphere_reg_wf")
 
     if t2w:
         t2w_template_wf = init_anat_template_wf(
diff --git a/smriprep/workflows/surfaces.py b/smriprep/workflows/surfaces.py
index 50c0ad8ae3..213552f203 100644
--- a/smriprep/workflows/surfaces.py
+++ b/smriprep/workflows/surfaces.py
@@ -494,7 +494,12 @@ def _dedup(in_list):
     return workflow
 
 
-def init_sphere_reg_wf(*, msm_sulc: bool = False, name: str = "sphere_reg_wf"):
+def init_sphere_reg_wf(
+    *,
+    msm_sulc: bool = False,
+    sloppy: bool = False,
+    name: str = "sphere_reg_wf",
+):
     """Generate GIFTI registration files to fsLR space"""
     from ..interfaces.surf import FixGiftiMetadata
     from ..interfaces.workbench import SurfaceSphereProjectUnproject
@@ -564,7 +569,7 @@ def init_sphere_reg_wf(*, msm_sulc: bool = False, name: str = "sphere_reg_wf"):
     fix_sphere_meta = pe.MapNode(
         FixGiftiMetadata(), iterfield='in_file', name='fix_sphere_meta',
     )
-    msm_sulc_wf = init_msm_sulc_wf()
+    msm_sulc_wf = init_msm_sulc_wf(sloppy=sloppy)
     # fmt:off
     workflow.connect([
         (get_surfaces, sphere_gii, [(('sphere', _sorted_by_basename), 'in_file')]),
@@ -578,7 +583,7 @@ def init_sphere_reg_wf(*, msm_sulc: bool = False, name: str = "sphere_reg_wf"):
     return workflow
 
 
-def init_msm_sulc_wf(*, name: str = 'msm_sulc_wf'):
+def init_msm_sulc_wf(*, sloppy: bool = False, name: str = 'msm_sulc_wf'):
     """Run MSMSulc registration to fsLR surfaces, per hemisphere."""
     from ..interfaces.msm import MSM
     from ..interfaces.workbench import SurfaceAffineRegression, SurfaceApplyAffine
@@ -618,8 +623,9 @@ def init_msm_sulc_wf(*, name: str = 'msm_sulc_wf'):
     # --indata=sub-${SUB}_ses-${SES}_hemi-${HEMI)_sulc.shape.gii \
     # --refdata=tpl-fsaverage_hemi-${HEMI}_den-164k_sulc.shape.gii \
     # --out=${HEMI}. --verbose
+    msm_conf = load_resource(f'msm/MSMSulcStrain{"Sloppy" if sloppy else "Final"}conf')
     msmsulc = pe.MapNode(
-        MSM(verbose=True, config_file=load_resource('msm/MSMSulcStrainFinalconf')),
+        MSM(verbose=True, config_file=msm_conf),
         iterfield=['in_mesh', 'reference_mesh', 'in_data', 'reference_data', 'out_base'],
         name='msmsulc',
         mem_gb=2,

From 4e6fdd3c85c9c9cc606e2307618bf36e60d2b8f9 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 6 Sep 2023 13:08:02 -0400
Subject: [PATCH 3/3] CI: Test sloppy MSM on CI

---
 .circleci/ds005_run.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.circleci/ds005_run.sh b/.circleci/ds005_run.sh
index 6981fe7478..864ea87f52 100644
--- a/.circleci/ds005_run.sh
+++ b/.circleci/ds005_run.sh
@@ -17,7 +17,6 @@ docker run -it -e FMRIPREP_DEV=1 -u $(id -u) \
     --skull-strip-template MNI152NLin2009cAsym:res-2 \
     --sloppy --mem-gb 4 \
     --ncpus 2 --omp-nthreads 2 -vv \
-    --no-msm \
     --fs-license-file /tmp/fslicense/license.txt \
     --fs-subjects-dir /tmp/ds005/freesurfer \
     ${@:1}