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1 | 1 | """ |
2 | 2 | The bidsmapper scans your source data repository to identify different data types by matching |
3 | 3 | them against the run-items in the template bidsmap. Once a match is found, a mapping to BIDS |
4 | | -output data types is made and the run-item is added to the study bidsmap. You can check and |
| 4 | +output data types is made and the run-item is added to the dataset bidsmap. You can check and |
5 | 5 | edit these generated bids-mappings to your needs with the (automatically launched) bidseditor. |
6 | 6 | Re-run the bidsmapper whenever something was changed in your data acquisition protocol and |
7 | 7 | edit the new data type to your needs (your existing bidsmap will be reused). |
@@ -33,14 +33,14 @@ def get_parser() -> argparse.ArgumentParser: |
33 | 33 | ' bidsmapper myproject/raw myproject/bids -p nibabel2bids # Uses a plugin of choice\n' |
34 | 34 | " bidsmapper myproject/raw myproject/bids -n patient- -m '*' # Handles DICOMDIR datasets\n" |
35 | 35 | " bidsmapper myproject/raw myproject/bids -u '*.tar.gz' # Unzip tarball source files\n ") |
36 | | - parser.add_argument('sourcefolder', help='The study root folder containing the raw source data folders') |
| 36 | + parser.add_argument('sourcefolder', help='The dataset root folder containing the raw source data folders') |
37 | 37 | parser.add_argument('bidsfolder', help='The destination folder with the (future) bids data and the bidsfolder/code/bidscoin/bidsmap.yaml output file') |
38 | | - parser.add_argument('-b','--bidsmap', help="The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the base name (i.e. no '/' in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml", metavar='NAME', default='bidsmap.yaml') |
| 38 | + parser.add_argument('-b','--bidsmap', help="The dataset bidsmap file with the mapping heuristics. If the bidsmap filename is just the base name (i.e. no '/' in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml", metavar='NAME', default='bidsmap.yaml') |
39 | 39 | parser.add_argument('-t','--template', help=f"The bidsmap template file with the default heuristics (this could be provided by your institute). If the bidsmap filename is just the base name (i.e. no '/' in the name) then it is assumed to be located in the bidscoin config folder. Default: {bidsmap_template.stem}", metavar='NAME', default=bidsmap_template) |
40 | | - parser.add_argument('-p','--plugins', help='List of plugins to be used. Default: the plugin list of the study/template bidsmap', nargs='+', metavar='NAME', default=[]) |
41 | | - parser.add_argument('-n','--subprefix', help="The prefix common for all the source subject-folders (e.g. 'Pt' is the subprefix if subject folders are named 'Pt018', 'Pt019', ...). Use '*' when your subject folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'sub-'", metavar='PREFIX') |
42 | | - parser.add_argument('-m','--sesprefix', help="The prefix common for all the source session-folders (e.g. 'M_' is the subprefix if session folders are named 'M_pre', 'M_post', ..). Use '*' when your session folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'ses-'", metavar='PREFIX') |
43 | | - parser.add_argument('-u','--unzip', help='Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the study/template bidsmap', metavar='PATTERN') |
| 40 | + parser.add_argument('-p','--plugins', help='List of plugins to be used. Default: the plugin list of the dataset/template bidsmap', nargs='+', metavar='NAME', default=[]) |
| 41 | + parser.add_argument('-n','--subprefix', help="The prefix common for all the source subject-folders (e.g. 'Pt' is the subprefix if subject folders are named 'Pt018', 'Pt019', ...). Use '*' when your subject folders do not have a prefix. Default: the value of the dataset/template bidsmap, e.g. 'sub-'", metavar='PREFIX') |
| 42 | + parser.add_argument('-m','--sesprefix', help="The prefix common for all the source session-folders (e.g. 'M_' is the subprefix if session folders are named 'M_pre', 'M_post', ..). Use '*' when your session folders do not have a prefix. Default: the value of the dataset/template bidsmap, e.g. 'ses-'", metavar='PREFIX') |
| 43 | + parser.add_argument('-u','--unzip', help='Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the dataset/template bidsmap', metavar='PATTERN') |
44 | 44 | parser.add_argument('-s','--store', help='Store newly discovered data samples in the bidsfolder/code/provenance folder (useful for editing e.g. zipped or DICOMDIR datasets)', action='store_true') |
45 | 45 | parser.add_argument('-a','--automated', help='Save the automatically generated bidsmap to disk and without interactively tweaking it with the bidseditor', action='store_true') |
46 | 46 | parser.add_argument('-f','--force', help='Discard the previously saved bidsmap and log file, instead of reusing them (use this option for a fresh start)', action='store_true') |
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