diff --git a/docs/faqs.md b/docs/faqs.md index 156c16fa..6476fe55 100644 --- a/docs/faqs.md +++ b/docs/faqs.md @@ -2,14 +2,14 @@ ## Leveraging precomputed results -Whether to allow for manual intervention for tough cases, or simply to reduce processing time, *NiBabies* can allow the use of certain pre-computed files during processing. -Initial support is limited to the following files: -- Anatomical mask in T1w space -- Antomical segmentation (aseg) in T1w space +Whether manual intervention is required, or you want to reduce processing time, *NiBabies* allow the use of certain pre-computed files during processing, which can skip part of the workflow. +Support is limited to the following files: +- Anatomical mask in T1w or T2w space +- Antomical segmentation (aseg) in T1w or T2w space To use pre-computed results, one or more [BIDS Derivatives](https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html#bids-derivatives) directories must be passed in to *NiBabies* using the `--derivatives` flag. Derivative directories must include a [`dataset_description.json` and the required fields](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#derived-dataset-and-pipeline-description). -Additionally, files must include the `space-orig` key-value pair in the name. +Additionally, files must include the `space-T1w` or `space-T2w` key-value pair in the filenames, and a matching sidecar JSON file with the `SpatialReference` field defined. A sample layout of a derivatives directory can be found below: @@ -18,11 +18,19 @@ my_precomputed/ ├── dataset_description.json └── sub-01 └── anat - ├── sub-01_space-orig_desc-aseg_dseg.nii.gz - ├── sub-01_space-orig_desc-brain_mask.json - └── sub-01_space-orig_desc-brain_mask.nii.gz + ├── sub-01_space-T2w_desc-aseg_dseg.json + ├── sub-01_space-T2w_desc-aseg_dseg.nii.gz + ├── sub-01_space-T2w_desc-brain_mask.json + └── sub-01_space-T2w_desc-brain_mask.nii.gz ``` +and the contents of the JSON files: +``` +{"SpatialReference": "sub-01/anat/sub-01_T2w.nii.gz"} +``` + +The `SpatialReference` file will be used to ensure the raw data and the derivatives are aligned and in the same space. + ## Multi-atlas segmentation with joint label fusion By default, *NiBabies* will run [FSL FAST](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST) for tissue segmentation, and Infant FreeSurfer for segmentation labels. @@ -53,4 +61,4 @@ In short, here is a quick heuristic on how new releases should be looked at: 1. If the `YY.MINOR` match the version you used, but the `MICRO` has changed, it is a bug-fix release. Check the [release notes](https://github.com/nipreps/nibabies/releases) - if the fixes do not pertain to your data, there is no need to upgrade. -For more in-depth information, refer to the [*NiPreps* release documentation](https://www.nipreps.org/devs/releases/#principles). \ No newline at end of file +For more in-depth information, refer to the [*NiPreps* release documentation](https://www.nipreps.org/devs/releases/#principles).