Here’s an upstream error might be relevant:
241107-13:24:13,437 nipype.workflow WARNING:
[Node] Error on "_msmsulc0" (/share/team/neuro-sci/Olivier_paste_here/work/fmriprep_24_1_wf/sub_00840065_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0)
241107-13:24:18,844 nipype.workflow ERROR:
Node _msmsulc0 failed to run on host fmriprep-0-1.
241107-13:24:18,989 nipype.workflow ERROR:
Saving crash info to /share/team/neuro-sci/Olivier_paste_here/sub-00840065/log/20241107-120832_6ef089e0-e558-4ec7-85dc-2549de0272db/crash-20241107-132418-cheouser-_msmsulc0-dce22bdb-8ee4-4efc-a833-33278c83617e.txt
Traceback (most recent call last):
File "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _msmsulc0.
And here is info from the associated crashfile (no other crashfiles):
Node: _msmsulc0
Working directory: /share/team/neuro-sci/Olivier_paste_here/work/fmriprep_24_1_wf/sub_00840065_wf/anat_fit_wf/msm_sulc_wf/msmsulc/mapflow/_msmsulc0
Node inputs:
args = <undefined>
config_file = /opt/fsl-6.0.7.7/lib/python3.11/site-packages/smriprep/data/msm/MSMSulcStrainFinalconf
environ = {}
in_data = /share/team/neuro-sci/Olivier_paste_here/work/fmriprep_24_1_wf/sub_00840065_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc0/sub-XYZ.L.sulc.native.shape.gii
in_mesh = /share/team/neuro-sci/Olivier_paste_here/work/fmriprep_24_1_wf/sub_00840065_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0/lh.sphere_converted_xformed.surf_mod.surf.gii
in_register = <undefined>
in_weight = <undefined>
levels = <undefined>
out_base = lh.
output_format = <undefined>
reference_data = /opt/fsl-6.0.7.7/lib/python3.11/site-packages/smriprep/data/atlases/L.refsulc.164k_fs_LR.shape.gii
reference_mesh = /opt/fsl-6.0.7.7/lib/python3.11/site-packages/smriprep/data/atlases/fsaverage.L_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 "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/fsl-6.0.7.7/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node _msmsulc0.
Cmdline:
msm --conf=/opt/fsl-6.0.7.7/lib/python3.11/site-packages/smriprep/data/msm/MSMSulcStrainFinalconf --indata=/share/team/neuro-sci/Olivier_paste_here/work/fmriprep_24_1_wf/sub_00840065_wf/anat_fit_wf/msm_sulc_wf/invert_sulc/mapflow/_invert_sulc0/sub-XYZ.L.sulc.native.shape.gii --inmesh=/share/team/neuro-sci/Olivier_paste_here/work/fmriprep_24_1_wf/sub_00840065_wf/anat_fit_wf/msm_sulc_wf/modify_sphere/mapflow/_modify_sphere0/lh.sphere_converted_xformed.surf_mod.surf.gii --out=lh. --refdata=/opt/fsl-6.0.7.7/lib/python3.11/site-packages/smriprep/data/atlases/L.refsulc.164k_fs_LR.shape.gii --refmesh=/opt/fsl-6.0.7.7/lib/python3.11/site-packages/smriprep/data/atlases/fsaverage.L_LR.spherical_std.164k_fs_LR.surf.gii --verbose
Stdout:
Stderr:
Part of FSL (ID: "")
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
Apologies for the large text, as I didn’t want to remove anything that might be relevant.