How to upgrade⚓︎

Upgrade to the latest version using your favorite method.

condapip

sam:~$ conda activate dcm2bids-dev
sam:~$ conda update dcm2bids

sam:~$ pip install --upgrade --force-reinstall dcm2bids

Binary executables now available

Tired of dealing with virtual envs in Python? You can now download executables directly from GitHub and use them right away. See Install dcm2bids for more info.

Upgrading from 2.x to 3.x⚓︎

This major release includes many new features that unfortunately requires breaking changes to configuration files.

Changes to existing description and config file keys⚓︎

Some "keys" had to be renamed in order to better align with the BIDS specification and reduce the risk of typos.

Description keys⚓︎

key before	key now
`dataType`	`datatype`
`modalityLabel`	`suffix`
`customLabels`	`custom_entities`
`sidecarChanges`	`sidecar_changes`
`intendedFor`	REMOVED

Configuration file keys⚓︎

key before	key now
`caseSensitive`	`case_sensitive`
`defaceTpl`	`post_op`
`searchMethod`	`search_method`
DOES NOT EXIST	`id`
DOES NOT EXIST	`extractor`

`sidecar_changes` : `intendedFor` and `id`⚓︎

intendedFor has two major changes:

Since intendedFor has always been a sidecar change under the hood, it now must be nested in sidecar_changes and will be treated as such. intendedFor is not a description key anymore.
Instead of relying on the index of an image listed in the config file as used to be done in dcm2bids version <= 2.1.9, intendedFor now works with the newly created id key. The id key needs to be added to the image the index was referring to in <= 2.1.9. the value for id must be an arbitrary string but must corresponds to the value for IntendedFor.

Refer to the id and IntendedFor documentation section for more info.

`custom_entities` and `extractors`⚓︎

Please check the custom_entities combined with extractors section for more information.

`post_op` now replaces `defaceTpl`⚓︎

Since a couple of versions, defaceTpl has been removed. Instead of just putting it back, we also generalized the whole concept of post operation. After being converted into nifti and before moving it to the BIDS structure people can now apply whatever script they want to run on their data.

Please check the post op section to get more info.

Last update: 2023-09-21
Created: 2023-07-16