Advanced configuration and commands⚓︎
How to use advanced configuration⚓︎
These optional configurations can be inserted in the configuration file at the
same level as the "description"
entry.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 |
|
custom_entities
combined with extractors⚓︎
default: None
extractors will allow you to extract information embedded into sidecar files. In the example above, it will try to match 2 different regex expressions (keys: task, run) within the SeriesDescription field and bodypart in BodyPartExamined field.
By using the same keys in custom_entities and if found, it will add this new
entities directly into the final filename. custom_entities can be a list that
combined extractor keys and regular entities. If key is task
it will
automatically add the field "TaskName" inside the sidecar file.
search_method
⚓︎
default: "search_method": "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.
dup_method
⚓︎
default: "dup_method": "run"
run is the default behavior and will add _run-
to the custom_entities of the
acquisition if it finds duplicate destination roots.
dup will keep the last duplicate description and put _dup-
to the
custom_entities of the other acquisitions. This behavior is a
heudiconv inspired
feature.
case_sensitive
⚓︎
default: "case_sensitive": "true"
If false, comparisons between strings/lists will be not case sensitive. It's
only disabled when used with "search_method": "fnmatch"
.
bids_uri
⚓︎
default: "bids_uri": "URI"
option: "bids_uri": "relative"
Using "bids_uri": "relative"
triggers the old behavior of dcm2bids (v2.1.9) that provides the path relative to within the subject directory without the BIDS URI (e.g., bids::sub-01/
). This option has been brought back for compatibility reasons, especially for fMRIprep users (pre v24.0.0).
post_op
⚓︎
default: "post_op": []
post_op key allows you to run any post-processing analyses just before moving the images to their respective directories.
For example, if you want to deface your T1w images you could use pydeface by adding:
1 2 3 4 5 6 7 8 9 10 11 |
|
It will specifically run the corresponding cmd
to any image that follow the
combinations datatype/suffix: (anat, T1w) or (anat, MP2RAGE)
.
How to use custom_entities
If you want to keep both versions of the same file (for example defaced and not defaced) you need to provide extra custom_entities otherwise it will keep only your script output.
Multiple post_op commands
Although you can add multiple commands, the combination datatype/suffix on which you want to run the command has to be unique. You cannot run multiple commands on a specific combination datatype/suffix.
1 2 3 4 5 6 7 |
|
In this example the second command my_new_script
will be running on any image
which datatype is fmap.
Finally, this is a template string and dcm2bids will replace src_file
and
dst_file
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.
criteria
⚓︎
Handle multi site filtering⚓︎
As mentioned in the first-steps tutorial, criteria is the way to filter specific acquisitions. If you work with dicoms from multiple sites you will need different criteria for the same kind of acquisition. In order to reduce the length of the config file, we developed a feature where for a specific criteria you can get multiple descriptions.
1 2 3 |
|
Enhanced float/int comparison⚓︎
Criteria can help you filter acquisitions by comparing float/int sidecar.
1 2 3 4 5 |
|
In this example, dcm2bids will check if RepetitionTime is lower or equal to 0.0086.
Here are the key coded to help you compare float/int sidecar.
key | operator |
---|---|
lt |
lower than |
le |
lower than or equal to |
gt |
greater than |
ge |
greater than or equal to |
btw |
between |
btwe |
between or equal to |
If you want to use btw or btwe you will need to give an ordered list like this.
1 2 3 4 5 |
|
How to use advanced commands⚓︎
dcm2bids advanced options⚓︎
By now, you should be used to getting the --help
information before running a
command.
1 |
|
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 |
|
--auto_extract_entities
⚓︎
This option will automatically try to find 3 entities (task, dir and echo) for specific datatype/suffix.
task
in the SeriesDescription field
Regular expression task-(?P<task>[a-zA-Z0-9]+)
dir
in the PhaseEncodedDirection field
Regular expression (?P<dir>-?j|i)
echo
in the EchoNumber field
Regular expression (?P<echo>[0-9])
If found, it will try to feed the filename with this entity if they are mandatory.
For example, a "pepolar" fieldmap data requires the entity dir
(See
BIDS specification).
If you set this parameter, it will automatically try to find this entity and add
it to the filename.
So far and accordingly to the BIDS specification 5 datatype/suffix automatically look for this 3 entities.
datatype | suffix | Entities |
---|---|---|
anat | MEGRE | echo |
anat | MESE | echo |
func | cbv | task |
func | bold | task |
func | sbref | task |
fmap | epi | dir |
Using the --auto_extract_entitie
, if you want another combination of
datatype/suffix to be able to extract one or more of these 3 entities you need
to add the key of the entities needed using the field custom_entities like this
within your description:
1 |
|
If task is found, it will automatically add the field TaskName
into
the sidecar file. It means you don't have to add the field in the config file
like this.
1 2 3 4 5 |
|
You can find more detailed information by looking at the file dcm2bids/utils/utils.py
and
more specifically auto_extractors
and auto_entities
variables.
You cannot use --auto_extract_entities
in conjunction with --do_not_reorder_entities
Refer to the Manuel ordering section for more information.
--do_not_reorder_entities
⚓︎
This option will keep the order of the entities as they are entered in the config file by the user in the custom_entities
field. However, please note that this flag cannot be used in conjunction with the --auto_extract_entities
flag.
--bids_validate
⚓︎
By default, dcm2bids will not validate your final BIDS structure. If needed, you can install bids-validator and activate this option.
--skip_dcm2niix
⚓︎
If you don't have access to original dicom files you can still use dcm2bids to reorganise your data into a BIDS structure. Using the option --skip_dcm2niix you will skip the conversion step.
Created: 2019-04-04