reg_trans_Composite.h5 not found

[isacdaavid]

Hi, I am testing your pipeline using a single subject. Dependencies have been installed. E,g, ants.

However the script gets stuck at this function ants_reg in myelin_map_funcs.py. This is the output:

python myelin_map_run.py 
Number of subjects to be processed: 1
Processing data for subj sub-A00000368
Directory /home/isaac/myelin_map/out exists. Not creating

Directory /home/isaac/myelin_map/out/sub-A00000368 already exists. Not creating.

Working dir: /home/isaac/myelin_map/out/sub-A00000368
sub-A00000368 {'t1': 1, 't2': 1}
240411-13:56:01,562 nipype.interface INFO:
	 stdout 2024-04-11T13:56:01.562138:ERROR:  Invalid flag provided use-estimate-learning-rate-once
240411-13:56:01,562 nipype.interface INFO:
	 stdout 2024-04-11T13:56:01.562138:ERROR:  Invalid flag provided use-estimate-learning-rate-once
240411-13:56:01,562 nipype.interface INFO:
	 stdout 2024-04-11T13:56:01.562138:ERROR:  Invalid flag provided use-estimate-learning-rate-once
240411-13:56:01,562 nipype.interface INFO:
	 stderr 2024-04-11T13:56:01.562350:ERROR:  Invalid command line flags found! Aborting execution.
Traceback (most recent call last):
  File "/home/isaac/Documents/school/6-phd/wisc/miniconda3/envs/myelin/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
    setattr(outputs, key, val)
  File "/home/isaac/Documents/school/6-phd/wisc/miniconda3/envs/myelin/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/home/isaac/Documents/school/6-phd/wisc/miniconda3/envs/myelin/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/home/isaac/Documents/school/6-phd/wisc/miniconda3/envs/myelin/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'composite_transform' trait of a RegistrationOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/home/isaac/myelin_map/out/sub-A00000368/reg_trans_Composite.h5' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/isaac/myelin_map/myelin_map_run.py", line 51, in <module>
    myelin_map_proc(subj = subj_dirs[0], n_cores = n_cores, raw_dir = raw_dir, output_dir = output_dir, patterns = patterns, n_scans = n_scans, dcm_suffix = dcm_suffix, fwhm_list = fwhm_list)
  File "/home/isaac/myelin_map/myelin_map_funcs.py", line 727, in myelin_map_proc
    reg_output = ants_reg(fixed = t1_subj_nii, moving = t1_im_mni_fn, output_dir = out_subj_dir)
  File "/home/isaac/myelin_map/myelin_map_funcs.py", line 223, in ants_reg
    reg_results = reg.run()
  File "/home/isaac/Documents/school/6-phd/wisc/miniconda3/envs/myelin/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/isaac/Documents/school/6-phd/wisc/miniconda3/envs/myelin/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/home/isaac/myelin_map/out/sub-A00000368/reg_trans_Composite.h5' for output 'composite_transform' of a Registration interface