AliceJoubert

AIBL-to-BIDS converter is not warning the user when not converting some sessions

2

In AIBL-to-BIDS, there are two ways an image can be missing from the output : - It can happen that the converter chooses not to convert some images. Sometimes, images...

In Genfi-to-BIDS, writing the different metadata types of files is done in only one function : https://github.com/aramis-lab/clinica/blob/4247631b0b01c72f53eb15439afa4eb4a6b48ac0/clinica/converters/genfi_to_bids/_utils.py#L783-L873 Rather than having one big function which is not tested, it would be...

[ENH] Change long_id format

1

Close #1415 - Uses '+' as a separator - TODO : modify CI data names

[ENH] Harmonize the way to delete images with unwanted suffices after dcm2niix conversion over converters.

2

In converters using `dcm2nix` (cf. [list](https://aramislab.paris.inria.fr/clinica/docs/public/dev/Software/Third-party/#converters) in the documentation), images are sometimes produced with a suffix indicating the image should _not_ be kept as clinica outputs. Known suffixes include :...

Documentation Refactoring Description

2

## Description The documentation of Clinica contains a lot of information scattered over different pages which can make it difficult for a user to navigate it or find relevant information....

[DOC] The outputs for some pipelines need to be clarified

3

In `PET-linear` : - [ ] What is obtained with or without option `-ui` is not intuitive. Currently, it says the cropped output is permanent while the uncropped one is...

Harmonize option `--subjects_list` over converters

1

Following #1467, converters for ADNI, OASIS1 and IXI should have the `-sl` option. Implementation was already different between ADNI and IXI, and OASIS1 added another one. Maybe this would be...

Broken MCR module on CI machines

4

Changing to clinica standalone set-up in CI with #1486 seems to have broken our non-regression tests : see https://github.com/aramis-lab/clinica/actions/workflows/test_non_regression_fast.yml Before : ```bash Loading clinica.all Loading requirement: clinica/ants/2.4.4 clinica/freesurfer/6.0.0 clinica/fsl/6.0.5 clinica/itk/4.13.0...

Improve tests for client instantiation

1

Recently several bugs linked to the client were reported (see #1480, #1484). These could have been avoided if the client was extensively tested. There is a [module](https://github.com/aramis-lab/clinica/blob/4fe58feabe9e3d7978348f3b090ae0c71fb89486/test/instantiation/test_cli.py) in instantiation tests...