How to use advanced commands and configuration
These optional configurations could be insert in the configuration file at the
same level as the "descriptions" entry.
{
"searchMethod": "fnmatch",
"caseSensitive": true,
"defaceTpl": ["pydeface", "--outfile", "dstFile", "srcFile"],
"description": [
...
]
}
searchMethod
default: "searchMethod": "fnmatch"
fnmatch is the behaviour (See criteria) by default and the fall back if this
option is set incorrectly. re is the other choice if you want more flexibility
to match criteria.
caseSensitive
default: "caseSensitive": "true"
If false, comparisons between strings/lists will be not case sensitive. It's
only disabled when used with "searchMethod": "fnmatch".
defaceTpl
default: "defaceTpl": None
!!! danger The anonymizer option no longer exists from v2.0.0. It is still
possible to deface the anatomical nifti images.
For example, if you use the last version of pydeface, add:
"defaceTpl": "pydeface --outfile {dstFile} {srcFile}"
It is a template string and dcm2bids will replace {srcFile} and {dstFile} by the source file (input) and the destination file (output).
dcm2niixOptions
default: "dcm2niixOptions": "-b y -ba y -z y -f '%3s_%f_%p_%t'"
Arguments for dcm2niix
compKeys
default: "compKeys": ["SeriesNumber", "AcquisitionTime", "SidecarFilename"]
Acquisitions are sorted using the sidecar data. The default behaviour is to sort
by SeriesNumber then by AcquisitionTime then by the SidecarFilename. You
can change this behaviour setting this key inside the configuration file.
Created: 2019-04-04