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.

{
  "extractors": {
    "SeriesDescription": [
      "run-(?P<run>[0-9]+)",
      "task-(?P<task>[0-9]+)"
    ],
    "BodyPartExamined": [
      "(?P<bodypart>[a-zA-Z]+)"
    ]
  },
  "search_method": "fnmatch",
  "case_sensitive": true,
  "dup_method": "dup",
  "post_op": [
    {
      "cmd": "pydeface --outfile dst_file src_file",
      "datatype": "anat",
      "suffix": [
        "T1w",
        "MP2RAGE"
      ],
    "custom_entities": "rec-defaced"
    }
  ],
  "descriptions": [
    {
      "datatype": "anat",
      "suffix": "T2w",
      "custom_entities": [
        "acq-highres",
        "bodypart",
        "run",
        "task"
      ],
      "criteria": ...
    }
  ]
}

`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 sidecase 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 customEntities of the acquisition if it finds duplicate destination roots.

dup will keep the last duplicate description and put _dup-to the customEntities 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".

`post_op`⚓︎

default: "post_op": []

post_op key allows you to run any post-processing analyses just before moving the images to there respective directories.

For example, if you want to deface your T1w images you could use pydeface by adding:

"post_op": [
  {
    "cmd": "pydeface --outfile dst_file src_file",
    "datatype": "anat",
    "suffix": [
      "T1w",
      "MP2RAGE"
    ],
    "custom_entities": "rec-defaced"
  }
],

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.

"post_op": [{"cmd": "pydeface --outfile dst_file src_file",
            "datatype": "anat",
            "suffix": ["T1w", "MP2RAGE"],
            "custom_entities": "rec-defaced"},
            {"cmd": "my_new_script --input src_file --output dst_file ",
            "datatype": "fmap",
            "suffix": ["any"]}],

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.

"criteria": {
    "SeriesDescription": {"any" : ["*MPRAGE*", "*T1w*"]}
}

Enhanced float/int comparison⚓︎

Criteria can help you filter acquisitions by comparing float/int sidecar.

"criteria": {
    "RepetitionTime": {
        "le": "0.0086"
    }
}

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.

"criteria": {
    "EchoTime": {
        "btwe": ["0.0029", "0.003"]
    }
}

How to use advanced commands⚓︎

dcm2bids advanced options⚓︎

By now, you should be used to getting the --help information before running a command.

CommandOutput

1	`dcm2bids --help`

(dcm2bids) sam:~/dcm2bids-tutorial/bids_project$ dcm2bids --help
usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR]
                [--auto_extract_entities] [--bids_validate] [--force_dcm2bids] [--skip_dcm2niix] [--clobber]
                [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
dcm2bids 3.0.0

options:
-h, --help            show this help message and exit
-d DICOM_DIR [DICOM_DIR ...], --dicom_dir DICOM_DIR [DICOM_DIR ...]
                        DICOM directory(ies)
-p PARTICIPANT, --participant PARTICIPANT
                        Participant ID
-s SESSION, --session SESSION
                        Session ID
-c CONFIG, --config CONFIG
                        JSON configuration file (see example/config.json)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
                        Output BIDS directory, Default: current directory (/home/sam/dcm2bids-tutorial/bids_project)
--auto_extract_entities If set, it will automatically try to extract entity information [task, dir, echo]
                        depending on the suffix and datatype. [False]
--bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
                      bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
--force_dcm2bids       Overwrite previous temporary dcm2bids output if it exists.
--skip_dcm2niix       Skip dcm2niix conversion. Option -d should contains NIFTI and json files.
--clobber             Overwrite output if it exists.
-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        Set logging level

            Documentation at https://github.com/unfmontreal/Dcm2Bids

`--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:

"custom_entities": ["echo", "dir"]

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
{ "sidecar_changes": { "TaskName": "learning" } }

You can find more detailed information by looking at the file dcm2bids/utils/utils.py and more specifically auto_extractors and auto_entities variables.

`--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.

Last update: 2023-09-12
Created: 2019-04-04

Advanced configuration and commands⚓︎

How to use advanced configuration⚓︎

custom_entities combined with extractors⚓︎

search_method⚓︎

dup_method⚓︎

case_sensitive⚓︎

post_op⚓︎

dcm2niixOptions⚓︎

compKeys⚓︎

criteria⚓︎