How to create a configuration file⚓︎
Configuration file example⚓︎
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The descriptions
field is a list of descriptions, each describing some
acquisition. In this example, the configuration describes five acquisitions, a
T2-weighted, a resting-state fMRI, a fieldmap, and an fMRI learning task with
another fieldmap.
Each description tells dcm2bids how to group a set of acquisitions and how to label them. In this config file, Dcm2Bids is being told to collect files containing
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in their sidecars1 and label them as anat
, T2w
type images.
criteria⚓︎
dcm2bids will try to match the sidecars1 of dcm2niix to the descriptions of the configuration file. The values you enter inside the criteria dictionary are patterns that will be compared to the corresponding key of the sidecar.
The pattern matching is shell-style. It's possible to use wildcard *
, single
character ?
etc ... Please have a look at the GNU documentation
to know more.
For example, in the second description, the pattern *T2*
will be compared to
the value of SeriesDescription
of a sidecar. AXIAL_T2_SPACE
will be a match,
AXIAL_T1
won't.
dcm2bids
has a SidecarFilename
key, as in the first description, if you
prefer to also match with the filename of the sidecar. Note that filename are
subject to change depending on the dcm2niix version in use.
You can enter several criteria. All criteria must match for a description to be linked to a sidecar.
datatype⚓︎
It is a mandatory field. Here is a definition from bids v1.2.0
:
Data type - a functional group of different types of data. In BIDS we define six data types: func (task based and resting state functional MRI), dwi (diffusion weighted imaging), fmap (field inhomogeneity mapping data such as field maps), anat (structural imaging such as T1, T2, etc.), meg (magnetoencephalography), beh (behavioral).
suffix⚓︎
It is a mandatory field. It describes the modality of the acquisition like
T1w
, T2w
or dwi
, bold
.
custom_entities⚓︎
It is an optional field. For some acquisitions, you need to add information in
the file name. For resting state fMRI, it is usually task-rest
.
To know more on how to set these fields, read the BIDS specifications.
For a longer example of a Dcm2Bids config json, see here.
Note that the different bids labels must come in a very specific order to be bids valid filenames. If the custom_entities fields that are entered that are in the wrong order, then dcm2bids will reorder them for you.
For example if you entered:
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when running dcm2bids, you will get the following warning:
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custom_entities could also be combined with extractors. See custom_entities combined with extractors
sidecar_changes, id and IntendedFor⚓︎
Optional field to change or add information in a sidecar.
IntendedFor
is now considered a sidecar_changes.
Example:
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If you want to add an IntendedFor
entry or any extra sidecar linked to a
specific file, you will need to set an id to the corresponding description and
put the same id with IntendedFor
.
For example, task_rest
means it is intended for task-rest_bold
and
id_task_learning
is intended for task-learning_bold
.
You could also use this feature to feed sidecar such as `Source`` for example or anything that suits your needs.
Multiple config files⚓︎
It is possible to create multiple config files and iterate the dcm2bids
command over the different config files to structure data that have different
parameters in their sidecar files.
-
For each acquisition,
dcm2niix
creates an associated.json
file, containing information from the dicom header. These are known as sidecars. These are the sidecars thatdcm2bids
uses to filter the groups of acquisitions.To define the filters you need, you will probably have to review these sidecars. You can generate all the sidecars for an individual participant using the dcm2bids_helper command. ↩↩
Created: 2022-04-19