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Maybe have a way to support this kind of usage:
Very simple single image -> output folder CLI (kind of like recon-all, except not implicitly using env var for subjects_dir)
hippunfold-<simple/single/subject/T1w> /path/to/my_input_t1.nii.gz /path/to/my/output_folder --subject 001 (--session ses)
internally, we would copy: my_input_t1.nii.gz to: bids/sub-001/anat/sub-001_T1.nii.gz
my_input_t1.nii.gz
bids/sub-001/anat/sub-001_T1.nii.gz
output folder can be: output_folder/sub-001
This might be best as a snakebids plugin.
plugin would need to know what are the required arguments, and how do they map to the app itself..
The text was updated successfully, but these errors were encountered:
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Maybe have a way to support this kind of usage:
Very simple single image -> output folder CLI
(kind of like recon-all, except not implicitly using env var for subjects_dir)
internally, we would copy:
my_input_t1.nii.gz
to:bids/sub-001/anat/sub-001_T1.nii.gz
output folder can be:
output_folder/sub-001
This might be best as a snakebids plugin.
plugin would need to know what are the required arguments, and how do they map to the app itself..
The text was updated successfully, but these errors were encountered: