I was trying to run TractoFlow on my dataset using Singularity. I’m using a BIDS-compliant dataset and defaults for all settings.
I can get all the way through Eddy/TOPUP and then I get an error message (just running for a single subject for the sake of ease):
[7e/586549] NOTE: Process `Normalize_DWI (sub-omega002_ses-bline_run-1)` terminated with an error exit status (1) -- Execution is retried (1)
[42/28a8ba] NOTE: Process `Normalize_DWI (sub-omega002_ses-bline_run-1)` terminated with an error exit status (1) -- Execution is retried (2)
[00/6d91f5] NOTE: Process `Normalize_DWI (sub-omega002_ses-bline_run-1)` terminated with an error exit status (1) -- Execution is retried (3)
[70/4f5041] NOTE: Process `Normalize_DWI (sub-omega002_ses-bline_run-1)` terminated with an error exit status (1) -- Error is ignored
No other information is give. Is there a way to debug this?
You will have more information about the issue if you look at this file: work/7e/586549*/.command.err
You can copy paste the information here so we can help you.
Thanks for pointing me in the right direction. Here’s the traceback:
Traceback (most recent call last):
File "/usr/local/bin/scil_compute_dti_metrics.py", line 4, in <module>
__import__('pkg_resources').run_script('scilpy==1.1', 'scil_compute_dti_metrics.py')
File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py", line 1464, in run_script
exec(code, namespace, namespace)
File "/usr/local/lib/python3.7/dist-packages/scilpy-1.1-py3.7-linux-x86_64.egg/EGG-INFO/scripts/scil_compute_dti_metrics.py", line 457, in <module>
main()
File "/usr/local/lib/python3.7/dist-packages/scilpy-1.1-py3.7-linux-x86_64.egg/EGG-INFO/scripts/scil_compute_dti_metrics.py", line 176, in main
mask = get_data_as_mask(nib.load(args.mask), dtype=bool)
File "/usr/local/lib/python3.7/dist-packages/scilpy-1.1-py3.7-linux-x86_64.egg/scilpy/io/image.py", line 73, in get_data_as_mask
'with a mask'.format(basename, curr_type))
OSError: The image sub-omega002_ses-bline_run-1__b0_mask_cropped.nii.gz cannot be loaded as mask because its type <class 'numpy.float32'> is not compatible with a mask
