Merge pull request #366 from effigies/test/msm-sloppy

TEST: Add sloppy MSM configuration for use in debugging/CI

Author: mgxd

.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}

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

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(

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,