omar-rifai
omar-rifai
### Objective Formalizing a way to store `freesurfer` outputs in a `BIDS` compliant hierarchy. In other words, the objective is **not** to make every `freesurfer` file `BIDS` compliant, but rather...
Hello, This is a small example of an output that could be obtained from the "t1freesurfer" pipeline from Clinica. Currently the directory hierarchy is a bit different but we are...
Initial implementation of T1Volume Tissue Segmentation with Pydra - [x] Write core workflow in Pydra - [x] Successfully execute with `@clinica_io` - [x] Integrate in hidden command line - [x]...
WIP towards a traceability feature for Clinica: - [x] Define data model for PROV concepts - [x] Serialize and de-serialize json-ld documents - [x] Compose prov modules with pipelines -...
as defined in [BEP011](https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y/edit#), we need to replace `_probability` suffix by `_probseg`.
- The [BIDS spec](https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html#res) imposes the definition of a metadata field for the `res` entity to "provide interpretation". - Also if only one label value for the `space` entity is...
The `_affine` suffix is not defined in the bids specs and a possible alternative (as per [BEP014](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE/edit#heading=h.y6haspjxjylp)) would be `_xfm` (to be confirmed).
- `target` should be replaced by `to-` and `from-` defined in [BEP014](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE/edit#heading=h.mqkmyp254xh6) to indicate a transformation from a "space" to another - Remove transformation-{inverse|forward} becomes superfluous if we use `to`...
- `modulated` is used in Clinica to indicate whether "modulation has been used in SPM to compensate for the effect of spatial normalization." (c.f documentation). This would likely need to...
as per [BEP016](https://github.com/bids-standard/bids-bep016/blob/bep-016/src/05-derivatives/05-diffusion-derivatives.md), we need to use the entity `parameter` with labels (FA | MD | AD ..) instead of having `FA`, `MD` etc as suffixes.