Invalid argument ``--regoption`` passed to MSM

[oesteban]

Describe the bug
A clear and concise description of what the bug is.

Exact command line executed

dmriprep blah blah

Are you positive that the input dataset is BIDS-compliant?

• I have used the online BIDS-Validator
• I have run a local installation of the BIDS-Validator (please, note the version of the validator here).
• I let sMRIPrep check it for me (in other words, I didn't set the --skip-bids-validation argument).
• No, I haven't checked myself AND used the --skip-bids-validation argument.

sMRIPrep feedback information
Please attach the full log written to the standard output and the crashfile(s), if generated.

Node: _msmsulc1
Working directory: /home/oesteban/tmp/dmriprep-tests/dmriprep-work/dmriprep_25_0_wf/sub_05_ses_JHU1-MGH1_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc1

Node inputs:

args = <undefined>
config_file = /home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/smriprep/data/msm/MSMSulcStrainFinalconf
environ = {}
in_data = /home/oesteban/tmp/dmriprep-tests/dmriprep-work/dmriprep_25_0_wf/sub_05_ses_JHU1-MGH1_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc1/sub-XYZ.R.sulc.native.shape.gii
in_mesh = /home/oesteban/tmp/dmriprep-tests/dmriprep-work/dmriprep_25_0_wf/sub_05_ses_JHU1-MGH1_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1/sub-05_hemi-R_sphere.surf_xformed.surf_mod.surf.gii
in_register = <undefined>
in_weight = <undefined>
levels = <undefined>
out_base = rh.
output_format = <undefined>
reference_data = /home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/smriprep/data/atlases/R.refsulc.164k_fs_LR.shape.gii
reference_mesh = /home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/smriprep/data/atlases/fsaverage.R_LR.spherical_std.164k_fs_LR.surf.gii
reference_weight = <undefined>
smooth_output_sigma = <undefined>
transformed_mesh = <undefined>
verbose = True

Traceback (most recent call last):
  File "/home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
                       ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
  File "/home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
           ~~~~~~~~~~~~~~~~~^^^^^^^^^
  File "/home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _msmsulc1.

Cmdline:
	msm --conf=/home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/smriprep/data/msm/MSMSulcStrainFinalconf --indata=/home/oesteban/tmp/dmriprep-tests/dmriprep-work/dmriprep_25_0_wf/sub_05_ses_JHU1-MGH1_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc1/sub-XYZ.R.sulc.native.shape.gii --inmesh=/home/oesteban/tmp/dmriprep-tests/dmriprep-work/dmriprep_25_0_wf/sub_05_ses_JHU1-MGH1_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere1/sub-05_hemi-R_sphere.surf_xformed.surf_mod.surf.gii --out=rh. --refdata=/home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/smriprep/data/atlases/R.refsulc.164k_fs_LR.shape.gii --refmesh=/home/oesteban/.miniconda/envs/dmriprep/lib/python3.13/site-packages/smriprep/data/atlases/fsaverage.R_LR.spherical_std.164k_fs_LR.surf.gii --verbose
Stdout:

Stderr:

	Part of FSL (ID: 6.0.4:ddd0a010)
	msm configuration parameters 

	Usage: 


	Optional arguments (You may optionally specify one or more of):
		--opt	optimisation method. Choice of: AFFINE,DISCRETE (default)
		--simval	code for determining which similarty measure is used to assess cost during registration: options are 1) SSD; 2) pearsons correlation (default); 3) NMI;)
		--it	number of iterations at each resolution (default -–it=3,3,3)
		--sigma_in	smoothing parameter for input image (default --sigma_in=2,2,2)
		--sigma_ref	Sigma parameter - smoothing parameter for reference image  (set equal to sigma_in by default)
		--lambda	Lambda parameter - controls contribution of regulariser 
		--datagrid	DATA grid resolution (default --datagrid=5,5,5). If parameter = 0 then the native mesh is used.
		--CPgrid	Control point grid resolution (default --CPgrid=2,3,4)
		--SGgrid	Sampling grid resolution (default = 2 levels higher than the control point grid)
		--anatgrid	Anatomical grid resolution (default = 2 levels higher than the control point grid)
		--aKNN	Number of neighbours for estimation of kNN graph and alpha entropy measure (default --aKNN=5,5,5)
		--cutthr	Upper and lower thresholds for defining cut vertices (default --cutthr=0,0)
		--mInt	Method used for mesh interpolations, options: TPS or BARY (default)
		--dInt	Method used for data interpolations, options: GAUSSIAN or ADAP_BARY (default)
		--regexp	Regulariser exponent 'rexp' (default 2.0)
		--weight	weight regulariser cost using areal distortion weighting
		--anorm	norm regulariser cost using mean angle (for HCP compatibility)
		--rescaleL	rescale label grid rather than using barycentres
		--log	log transform and normalise the data
		--IN	Normalize intensity ranges using histogram matching 
		--INc	Normalize intensity ranges using histogram matching excluding cut
		--VN	Variance normalize data 
		--scale	Scale intensity ranges of a features in multivariate data to be equal to that of the first (useful for multimodal contrasts)
		--excl	Ignore the cut when resampling the data
		--stepsize	gradient stepping for affine optimisation (default 0.01)
		--gradsampling	Determines the finite distance spacing for the affine gradient calculation (default 0.5)
		--numthreads	number of threads for tbb (default 1)



	--regoption: Option doesn't exist!
Traceback:
	RuntimeError: subprocess exited with code 1.

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Installation type (please complete the following information):

• "Bare-metal"
• Singularity
• Docker

Additional context
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[oesteban]

This seems to be the offending line:

smriprep/src/smriprep/data/msm/MSMSulcStrainFinalconf

Line 10 in f588b83

--regoption=3

[effigies]

Guessing you're not using the same MSM? They haven't been very good at keeping a consistent CLI.

smriprep/Dockerfile

Lines 170 to 171 in f588b83

	RUN curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/ecr05/MSM_HOCR/releases/assets/16253707 -o /usr/local/bin/msm \
	&& chmod +x /usr/local/bin/msm

[oesteban]

Sure I'm not, thanks for the tip. I don't know how I feel about recovering from this error (and remove the option).

[oesteban]

For the record, this is the MSM version I had installed (FSL 6.0.4):

$ /opt/fsl/bin/msm.original -p

Part of FSL (ID: 6.0.4:ddd0a010)
msm configuration parameters 

Usage: 


Optional arguments (You may optionally specify one or more of):
	--opt	optimisation method. Choice of: AFFINE,DISCRETE (default)
	--simval	code for determining which similarty measure is used to assess cost during registration: options are 1) SSD; 2) pearsons correlation (default); 3) NMI;)
	--it	number of iterations at each resolution (default -–it=3,3,3)
	--sigma_in	smoothing parameter for input image (default --sigma_in=2,2,2)
	--sigma_ref	Sigma parameter - smoothing parameter for reference image  (set equal to sigma_in by default)
	--lambda	Lambda parameter - controls contribution of regulariser 
	--datagrid	DATA grid resolution (default --datagrid=5,5,5). If parameter = 0 then the native mesh is used.
	--CPgrid	Control point grid resolution (default --CPgrid=2,3,4)
	--SGgrid	Sampling grid resolution (default = 2 levels higher than the control point grid)
	--anatgrid	Anatomical grid resolution (default = 2 levels higher than the control point grid)
	--aKNN	Number of neighbours for estimation of kNN graph and alpha entropy measure (default --aKNN=5,5,5)
	--cutthr	Upper and lower thresholds for defining cut vertices (default --cutthr=0,0)
	--mInt	Method used for mesh interpolations, options: TPS or BARY (default)
	--dInt	Method used for data interpolations, options: GAUSSIAN or ADAP_BARY (default)
	--regexp	Regulariser exponent 'rexp' (default 2.0)
	--weight	weight regulariser cost using areal distortion weighting
	--anorm	norm regulariser cost using mean angle (for HCP compatibility)
	--rescaleL	rescale label grid rather than using barycentres
	--log	log transform and normalise the data
	--IN	Normalize intensity ranges using histogram matching 
	--INc	Normalize intensity ranges using histogram matching excluding cut
	--VN	Variance normalize data 
	--scale	Scale intensity ranges of a features in multivariate data to be equal to that of the first (useful for multimodal contrasts)
	--excl	Ignore the cut when resampling the data
	--stepsize	gradient stepping for affine optimisation (default 0.01)
	--gradsampling	Determines the finite distance spacing for the affine gradient calculation (default 0.5)
	--numthreads	number of threads for tbb (default 1)

and this is the one we're using (FSL 6.0.2):

$ /opt/fsl/bin/msm -p

Part of FSL (ID: 6.0.2:a4f562d9)
msm configuration parameters 

Usage: 


Optional arguments (You may optionally specify one or more of):
	--opt	optimisation method. Choice of: AFFINE,DISCRETE (default)
	--simval	code for determining which similarty measure is used to assess cost during registration: options are 1) SSD; 2) pearsons correlation (default); 3) NMI;)
	--it	number of iterations at each resolution (default -–it=3,3,3)
	--sigma_in	smoothing parameter for input image (default --sigma_in=2,2,2)
	--sigma_ref	Sigma parameter - smoothing parameter for reference image  (set equal to sigma_in by default)
	--lambda	Lambda parameter - controls contribution of regulariser 
	--datagrid	DATA grid resolution (default --datagrid=5,5,5). If parameter = 0 then the native mesh is used.
	--CPgrid	Control point grid resolution (default --CPgrid=2,3,4)
	--SGgrid	Sampling grid resolution (default = 2 levels higher than the control point grid)
	--anatgrid	Anatomical grid resolution (default = 2 levels higher than the control point grid)
	--aKNN	Number of neighbours for estimation of kNN graph and alpha entropy measure (default --aKNN=5,5,5)
	--cutthr	Upper and lower thresholds for defining cut vertices (default --cutthr=0,0)
	--mInt	Method used for mesh interpolations, options: TPS or BARY (default)
	--dInt	Method used for data interpolations, options: GAUSSIAN or ADAP_BARY (default)
	--regoption	Choose option for regulariser form lambda*weight*pow(cost,rexp). Where cost can be PAIRWISE or TRI-CLIQUE based. Options are: 1) PAIRWISE - penalising diffences in rotations of neighbouring points (default); 2) TRI_CLIQUE Angle deviation penalty (for spheres); 3) TRI_CLIQUE: Strain-based (for spheres);  4) TRI_CLIQUE Angle deviation penalty (for anatomy); 5) TRI_CLIQUE: Strain-based (for anatomy)
	--triclique	estimate similarity for triangular patches (rather than circular)
	--shearmod	shear modulus (default 0.4); for use with --regoptions 3 
	--bulkmod	bulk mod (default 1.6); for use with --regoptions 3 
	--k_exponent	exponent inside strain equation (default 2)
	--regexp	Regulariser exponent 'rexp' (default 2.0)
	--weight	weight regulariser cost using areal distortion weighting
	--anorm	norm regulariser cost using mean angle (for HCP compatibility)
	--rescaleL	rescale label grid rather than using barycentres
	--log	log transform and normalise the data
	--IN	Normalize intensity ranges using histogram matching 
	--INc	Normalize intensity ranges using histogram matching excluding cut
	--VN	Variance normalize data 
	--scale	Scale intensity ranges of a features in multivariate data to be equal to that of the first (useful for multimodal contrasts)
	--excl	Ignore the cut when resampling the data
	--stepsize	gradient stepping for affine optimisation (default 0.01)
	--gradsampling	Determines the finite distance spacing for the affine gradient calculation (default 0.5)
	--numthreads	number of threads for tbb (default 1)