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DOC: BIDS filter input example #2028

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Mar 17, 2020
Merged

DOC: BIDS filter input example #2028

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177a84a
add section to faq and pointer in parser.py
utooley Mar 16, 2020
c832e60
pep8 and formatting fixes
utooley Mar 16, 2020
33f7ae7
fixed FAQ format that stopped tests
utooley Mar 16, 2020
3a40d97
Update docs/faq.rst
utooley Mar 17, 2020
1d718a1
DOC: pointer to filtering FAQ
mgxd Mar 17, 2020
82206ed
Apply suggestions from code review
utooley Mar 17, 2020
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37 changes: 37 additions & 0 deletions docs/faq.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -220,3 +220,40 @@ After getting the resources you'll need, you will just need to make sure your
runtime environment is able to access the filesystem, at the location of your
*TemplateFlow home* directory.
If you are a Singularity user, please check out :ref:`singularity_tf`.

How do I select only certain files to be input to fMRIPrep?
-----------------------------------------------------------

Using the ``--bids-filter-file`` flag, you can pass fMRIPrep a JSON file that
describes a custom BIDS filter for selecting files with PyBIDS, with the syntax
``{<query>: {<entity>: <filter>, ...},...}``. For example::

{
"t1w": {
"datatype": "anat",
"session": "02",
"acquisition": null,
"suffix": "T1w"
},
"bold": {
"datatype": "func",
"session": "02",
"suffix": "bold"
}
}

fMRIPrep uses the following queries, by default::

{
'fmap': {'datatype': 'fmap'},
'bold': {'datatype': 'func', 'suffix': 'bold'},
'sbref': {'datatype': 'func', 'suffix': 'sbref'},
'flair': {'datatype': 'anat', 'suffix': 'FLAIR'},
't2w': {'datatype': 'anat', 'suffix': 'T2w'},
't1w': {'datatype': 'anat', 'suffix': 'T1w'},
'roi': {'datatype': 'anat', 'suffix': 'roi'},
}

Only modifications of these queries will have any effect. You may filter on any entity defined
in the the PyBIDS
`config file <https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json>`__.
8 changes: 5 additions & 3 deletions fmriprep/cli/run.py
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Expand Up @@ -79,9 +79,11 @@ def get_parser():
# help='select a specific run to be processed')
g_bids.add_argument(
'--bids-filter-file', action='store', type=Path, metavar='PATH',
help='a JSON file describing custom BIDS input filter using pybids '
'{<suffix>:{<entity>:<filter>,...},...} '
'(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)')
help="a JSON file describing custom BIDS input filters using PyBIDS. "
"For further details, please check out "
"https://fmriprep.readthedocs.io/en/%s/faq.html#"
"how-do-I-select-only-certain-files-to-be-input-to-fMRIPrep" % (
currentv.base_version if is_release else 'latest'))
g_bids.add_argument('-t', '--task-id', action='store',
help='select a specific task to be processed')
g_bids.add_argument('--echo-idx', action='store', type=int,
Expand Down