Merge remote-tracking branch 'upstream/master' into next

Author: effigies

smriprep/interfaces/msm.py

@@ -44,7 +44,7 @@ class MSMInputSpec(CommandLineInputSpec):
         exists=True,
         argstr="--trans=%s",
         desc="Transformed source mesh (output of a previous registration). "
-        "Use this to initiliase the current registration.",
+        "Use this to initialise the current registration.",
     )
     in_register = File(
         exists=True,
@@ -87,7 +87,7 @@ class MSMInputSpec(CommandLineInputSpec):
     )
     smooth_output_sigma = traits.Int(
         argstr="--smoothout=%d",
-        desc="smooth tranformed output with this sigma (default=0)",
+        desc="smooth transformed output with this sigma (default=0)",
     )
     verbose = traits.Bool(
         argstr="--verbose",

smriprep/interfaces/workbench.py

@@ -352,6 +352,71 @@ class SurfaceApplyWarpfield(WBCommand):
     _cmd = "wb_command -surface-apply-warpfield"
 
 
+class SurfaceModifySphereInputSpec(CommandLineInputSpec):
+    in_surface = File(
+        exists=True,
+        mandatory=True,
+        position=0,
+        argstr="%s",
+        desc="the sphere to modify",
+    )
+    radius = traits.Int(
+        mandatory=True,
+        position=1,
+        argstr="%d",
+        desc='the radius the output sphere should have'
+    )
+    out_surface = File(
+        name_template="%s_mod.surf.gii",
+        name_source="in_surface",
+        position=2,
+        argstr="%s",
+        desc="the modified sphere",
+    )
+    recenter = traits.Bool(
+        False,
+        position=3,
+        argstr="-recenter",
+        desc="recenter the sphere by means of the bounding box",
+    )
+
+
+class SurfaceModifySphereOutputSpec(TraitedSpec):
+    out_surface = File(desc="the modified sphere")
+
+
+class SurfaceModifySphere(WBCommand):
+    """CHANGE RADIUS AND OPTIONALLY RECENTER A SPHERE
+
+    wb_command -surface-modify-sphere
+      <sphere-in> - the sphere to modify
+      <radius> - the radius the output sphere should have
+      <sphere-out> - output - the output sphere
+
+      [-recenter] - recenter the sphere by means of the bounding box
+
+    This command may be useful if you have used -surface-resample to resample
+    a sphere, which can suffer from problems generally not present in
+    -surface-sphere-project-unproject.  If the sphere should already be
+    centered around the origin, using -recenter may still shift it slightly
+    before changing the radius, which is likely to be undesireable.
+
+    If <sphere-in> is not close to spherical, or not centered around the
+    origin and -recenter is not used, a warning is printed.
+
+    >>> sms = SurfaceModifySphere()
+    >>> sms.inputs.in_surface = 'sub-01_hemi-L_sphere.surf.gii'
+    >>> sms.inputs.radius = 100
+    >>> sms.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    'wb_command -surface-modify-sphere \
+    sub-01_hemi-L_sphere.surf.gii 100 sub-01_hemi-L_sphere.surf_mod.surf.gii'
+    """
+
+    input_spec = SurfaceModifySphereInputSpec
+    output_spec = SurfaceModifySphereOutputSpec
+    _cmd = 'wb_command -surface-modify-sphere'
+
+
 class SurfaceSphereProjectUnprojectInputSpec(TraitedSpec):
     """COPY REGISTRATION DEFORMATIONS TO DIFFERENT SPHERE.
 

smriprep/workflows/surfaces.py

@@ -747,7 +747,11 @@ def init_fsLR_reg_wf(*, name="fsLR_reg_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
+    from ..interfaces.workbench import (
+        SurfaceAffineRegression,
+        SurfaceApplyAffine,
+        SurfaceModifySphere,
+    )
 
     workflow = Workflow(name=name)
     inputnode = pe.Node(
@@ -777,6 +781,14 @@ def init_msm_sulc_wf(*, sloppy: bool = False, name: str = 'msm_sulc_wf'):
         iterfield=['in_surface', 'in_affine'],
         name='apply_surface_affine',
     )
+
+    # Fix for oblongated sphere
+    modify_sphere = pe.MapNode(
+        SurfaceModifySphere(radius=100),
+        iterfield=['in_surface'],
+        name='modify_sphere',
+    )
+
     # 2) Run MSMSulc
     # ./msm_centos_v3 --conf=MSMSulcStrainFinalconf \
     # --inmesh=${SUB}.${HEMI}.sphere_rot.native.surf.gii
@@ -823,8 +835,9 @@ def init_msm_sulc_wf(*, sloppy: bool = False, name: str = 'msm_sulc_wf'):
                                      ('sphere_reg_fsLR', 'target_surface')]),
         (inputnode, apply_surface_affine, [('sphere', 'in_surface')]),
         (regress_affine, apply_surface_affine, [('out_affine', 'in_affine')]),
+        (apply_surface_affine, modify_sphere, [('out_surface', 'in_surface')]),
         (inputnode, msmsulc, [('sulc', 'in_data')]),
-        (apply_surface_affine, msmsulc, [('out_surface', 'in_mesh')]),
+        (modify_sphere, msmsulc, [('out_surface', 'in_mesh')]),
         (msmsulc, outputnode, [('warped_mesh', 'sphere_reg_fsLR')]),
     ])
     # fmt:on