v.2.3.1 / latest conda env osle: coregistration error: float expects a scalar #409
Description
Good morning,
I ran the batch with the latest version and got this error in the logs.
osl-ephys SOURCE RECON failed at: 2025-05-21 10:07:09
Processing failed during stage : "coregister"<class 'TypeError'>
only size-1 arrays can be converted to Python scalars
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/batch.py", line 248, in run_src_chain
wrapped_func(
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/batch.py", line 247, in wrapped_func
return func(**kwargs_to_pass)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/wrappers.py", line 412, in coregister
fid_err = rhino.coreg_metrics(subjects_dir=outdir, subject=subject)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/rhino/coreg.py", line 447, in coreg_metrics
coreg_error = float(coreg_error)
I fixed it by replacing line 447 with:
# handles arrays
coreg_error = float(coreg_error[0]) if hasattr(coreg_error, "__getitem__") else float(coreg_error)
Also got another error (simple missing package error)
osl-ephys SOURCE RECON failed at: 2025-05-21 10:22:24
Processing failed during stage : "coregister"<class 'ImportError'>
Please install pythreejs to use this feature
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/batch.py", line 248, in run_src_chain
wrapped_func(
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/batch.py", line 247, in wrapped_func
return func(**kwargs_to_pass)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/wrappers.py", line 418, in coregister
rhino.coreg_display(
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/rhino/coreg.py", line 777, in coreg_display
rhino_utils.save_or_show_renderer(renderer, filename)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/rhino/utils.py", line 986, in save_or_show_renderer
renderer.figure.plotter.export_html(filename)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/pyvista/plotting/plotting.py", line 525, in export_html
widget = self.to_pythreejs()
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/pyvista/plotting/plotting.py", line 571, in to_pythreejs
from pyvista.jupyter.pv_pythreejs import convert_plotter
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/pyvista/jupyter/pv_pythreejs.py", line 10, in
raise ImportError('Please install pythreejs to use this feature')
Installing the latest version of pythreejs fixed that.
I also got some fsl related error logs (mainly plotting stuff)
osl-ephys SOURCE RECON failed at: 2025-05-21 10:34:41
Processing failed during stage : "compute_surfaces"<class 'fsl.utils.path.PathError'>
Could not find a supported file with prefix "/home/carinaf/tms_mdd/source_reco_giles_parcel_strictest_rejection/199_4/rhino/surfaces/flirt_smri_mni.nii.gz"
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/batch.py", line 248, in run_src_chain
wrapped_func(
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/batch.py", line 247, in wrapped_func
return func(**kwargs_to_pass)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/wrappers.py", line 259, in compute_surfaces
already_computed = rhino.compute_surfaces(
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/osl_ephys/source_recon/rhino/surfaces.py", line 305, in compute_surfaces
fsl_wrappers.bet(flirt_smri_mni_file, flirt_smri_mni_bet_file, A=True)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 1215, in wrapper
result = fot(*args, **kwargs)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 854, in call
result = func(*args, **kwargs)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/wrappers/wrapperutils.py", line 202, in wrapper
cmd = func(*args, **kwargs)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/wrappers/bet.py", line 32, in bet
asrt.assertIsNifti(input)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/utils/assertions.py", line 70, in wrapper
return func(*args, **kwargs)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/utils/assertions.py", line 105, in assertIsNifti
f = ensure.ensureIsImage(f)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/utils/ensure.py", line 27, in ensureIsImage
img = fslimage.addExt(img)
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/data/image.py", line 1951, in addExt
raise e
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/data/image.py", line 1938, in addExt
return fslpath.addExt(prefix,
File "/home/carinaf/miniforge3/envs/osle/lib/python3.8/site-packages/fsl/utils/path.py", line 196, in addExt
raise PathError('Could not find a supported file '
Is there a recommended fsl version? The installed version on the cluster I am using is 6.0.5.
currently not working with the cloned repo, but I think I will from now on, so I can fix the stuff and send a PR, save both you and me time :)
Cheers,
Carina