Brainmask ingression broken for HCP data

[j1c]

Summary

I am getting a FileNotFoundError for bold brain mask when trying to process HCP data. I believe this is caused by #1473, as 0.11.0rc1 version runs for nifti format, but both 0.11.0 and 0.11.1 errors.

This block uses brainmask_fs.2.nii.gz

xcp_d/xcp_d/ingression/hcpya.py

Lines 276 to 281 in 402269a

	boldmask_nifti_orig = os.path.join(task_dir_orig, 'brainmask_fs.2.nii.gz')
	boldmask_nifti_fmriprep = os.path.join(
	func_dir_bids,
	f'{func_prefix}_{volspace_ent}_{RES_ENT}_desc-brain_mask.nii.gz',
	)
	copy_dictionary[boldmask_nifti_orig] = [boldmask_nifti_fmriprep]

but this block, which was added in #1473, only checks for brainmask_fs.2.0.nii.gz or brainmask_fs.nii.gz

xcp_d/xcp_d/ingression/hcpya.py

Lines 293 to 301 in 402269a

	bold_mask_orig = os.path.join(task_dir_orig, 'brainmask_fs.2.0.nii.gz')
	if not os.path.isfile(bold_mask_orig):
	bold_mask_orig = os.path.join(task_dir_orig, 'brainmask_fs.nii.gz')
	bold_mask_fmriprep = os.path.join(
	func_dir_bids,
	f'{func_prefix}_{volspace_ent}_{RES_ENT}_desc-brain_mask.nii.gz',
	)
	copy_dictionary[bold_mask_orig] = [bold_mask_fmriprep]

It is noted in #1460 that brainmask_fs.2.0.nii.gz files can exist, but I only have brainmask_fs.2.nii.gz files. Im not entirely sure of the difference between boldmask_nifti_fmriprep and bold_mask_fmriprep, but it seems like they should be pointing to the same file. Probably could just check once for the existence of brainmask_fs.2.0.nii.gz, brainmask_fs.2.nii.gz or brainmask_fs.nii.gz, and use that for both boldmask_nifti_fmriprep and bold_mask_fmriprep.

Additional details

• xcp_d version: 0.11.1

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/xcp_d", line 8, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/run.py", line 25, in main
    parse_args(args=sys.argv[1:])
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/parser.py", line 839, in parse_args
    convert_to_bids(
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/ingression/hcpya.py", line 107, in convert_hcp2bids
    convert_hcp_to_bids_single_subject(
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/ingression/hcpya.py", line 363, in convert_hcp_to_bids_single_subject
    copy_files_in_dict(copy_dictionary)
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/ingression/utils.py", line 383, in copy_files_in_dict
    copy_file(file_orig, file_fmriprep)
  File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/ingression/utils.py", line 395, in copy_file
    if not os.path.exists(dst) or not filecmp.cmp(src, dst):
  File "/usr/local/miniconda/lib/python3.10/filecmp.py", line 53, in cmp
    s1 = _sig(os.stat(f1))
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/t/hcpya/990366/MNINonLinear/Results/rfMRI_REST1_LR/brainmask_fs.nii.gz'

[tsalo]

I'm on vacation until Monday but if you're willing to open a PR I can review it.