Merge pull request #485 from LuciMoore/master

Add documentation on MCRIBS and surf recon methods chosen based on age

Author: mgxd

docs/outputs.md

@@ -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.
@@ -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.

docs/usage.md

@@ -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.