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Sep 16, 2025
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Add documentation on MCRIBS and surf recon methods chosen based on age #485

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0e43dd3
Update usage.md
LuciMoore Sep 16, 2025
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Update outputs.md
LuciMoore Sep 16, 2025
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4 changes: 3 additions & 1 deletion docs/outputs.md
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Expand Up @@ -194,7 +194,7 @@ TODO: FSDERIVS? .. _fsderivs:

### Surface Reconstruction

If any of the surface reconstruction methods are enabled,
If any of the surface reconstruction methods (M-CRIB-S, infant FreeSurfer, or FreeSurfer) are enabled,
then a FreeSurfer-like subjects directory is created in
`<output dir>/sourcedata/freesurfer` or the directory indicated with the
`--fs-subjects-dir` flag.
Expand Down Expand Up @@ -229,6 +229,8 @@ This is strictly true when pre-computed FreeSurfer derivatives are provided eith
the `sourcedata/` directory or passed via the `--fs-subjects-dir` flag;
if NiBabies runs FreeSurfer, then there is a mutual dependency.

**If M-CRIB-S is used** for surface reconstruction, an additional folder is created in `<output dir>/sourcedata/mcribs`. M-CRIB-S converts and organizes its output into a FreeSurfer-compatible format, i.e. following the structure of FreeSurfer’s [recon-all](https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles), to `mcribs/sub-<label>_ses-<label>/freesurfer/`. This is then mapped by Infant fMRIPrep into the `sourcedata/freesurfer/` folder for further processing.

### Functional derivatives

Functional derivatives are stored in the `func/` subfolder.
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6 changes: 6 additions & 0 deletions docs/usage.md
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Expand Up @@ -22,6 +22,12 @@ Specifically, these two files will be checked:
Either file should include `age` (or if you wish to be more explicit: `age_months`) columns, and it is
recommended to have an accompanying JSON file to further describe these fields, and explicitly state the values are in months.

Age is used to choose the optimal surface reconstruction method when the flag `--surface-recon-method auto` is employed for surface reconstruction:

- M-CRIB-S: 0-3 months old (only if T2w and segmentation in T2w space is present)
- infant FreeSurfer: 4-24 months old (or 0-24 months old if no T2w/T2w segmentation is present)
- FreeSurfer (standard FreeSurfer developed from adult data): >24 months old

## The FreeSurfer license

*NiBabies* uses FreeSurfer tools, which require a license to run.
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