DOC: Update documentation to reflect --age-months deprecation [skip ci]

Author: mgxd

docs/usage.md

@@ -8,21 +8,19 @@ The input dataset is required to be in valid
 {abbr}`BIDS (The Brain Imaging Data Structure)` format,
 and it must include at least one T1-weighted and
 one T2-weighted structural image and
-(unless disabled with a flag) a BOLD series.
+a BOLD series (unless using the `--anat-only` flag).
+
 We highly recommend that you validate your dataset with the free, online
 [BIDS Validator](http://bids-standard.github.io/bids-validator/).
 
-The exact command to run *NiBabies* depends on the [Installation](./installation.md) method.
-The common parts of the command follow the
-[BIDS-Apps](https://github.com/BIDS-Apps) definition.
-Example:
-
-```Shell
-$ nibabies data/bids_root/ out/ participant -w work/ --participant-id 01 --age-months 12
-```
+### Participant Ages
+*NiBabies* will attempt to automatically extract participant ages (in months) from the BIDS layout.
+Specifically, these two files will be checked:
+- [Sessions file](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#sessions-file): `<bids-root>/<subject>/subject_sessions.tsv`
+- [Participants file](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file): `<bids-root>/participants.tsv`
 
-Further information about BIDS and BIDS-Apps can be found at the
-[NiPreps portal](https://www.nipreps.org/apps/framework/).
+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.
 
 ## The FreeSurfer license
 
@@ -33,6 +31,21 @@ To obtain a FreeSurfer license, simply register for free at https://surfer.nmr.m
 FreeSurfer will search for a license key file first using the `$FS_LICENSE` environment variable and then in the default path to the license key file (`$FREESURFER_HOME`/license.txt). If `$FS_LICENSE` is set, the [`nibabies-wrapper`](#using-the-nibabies-wrapper) will automatically handle setting the license within the container.
 Otherwise, you will need to use the `--fs-license-file` flag to ensure the license is available.
 
+
+## Example command
+
+The exact command to run *NiBabies* depends on the [Installation](./installation.md) method.
+The common parts of the command follow the
+[BIDS-Apps](https://github.com/BIDS-Apps) definition.
+Example:
+
+```Shell
+$ nibabies data/bids_root/ out/ participant -w work/ --participant-id 01
+```
+
+Further information about BIDS and BIDS-Apps can be found at the
+[NiPreps portal](https://www.nipreps.org/apps/framework/).
+
 ## Command-Line Arguments
 ```{argparse}
 :ref: nibabies.cli.parser._build_parser
@@ -50,21 +63,9 @@ At minimum, the following *positional* arguments are required.
 
 However, as infant brains can vastly differ depending on age, providing the following arguments is highly recommended:
 
-- **`--age-months`** - participant age in months
-
-:::{admonition} Warning
-:class: warning
-
-This is required if FreeSurfer is not disabled (`--fs-no-reconall`)
-:::
-
 - **`--participant-id`** - participant ID
 
-:::{admonition} Tip
-:class: tip
-
-This is recommended when using `--age-months` if age varies across participants.
-:::
+- **`--session-id`** - session ID
 
 - **`--segmentation-atlases-dir`** - directory containing pre-labeled segmentations to use for Joint Label Fusion.
 
@@ -85,11 +86,11 @@ For installation instructions, please see [](installation.md#installing-the-niba
 ### Sample Docker usage
 
 ```
-$ nibabies-wrapper docker /path/to/data /path/to/output participant --age-months 12 --fs-license-file /usr/freesurfer/license.txt
+$ nibabies-wrapper docker /path/to/data /path/to/output participant --fs-license-file /usr/freesurfer/license.txt
 
 RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.6 -it -v /path/to/data:/data:ro \
 -v /path/to/output:/out -v /usr/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
-nipreps/nibabies:21.0.0 /data /out participant --age-months 12
+nipreps/nibabies:23.0.0 /data /out participant
 ...
 ```
 
@@ -103,11 +104,11 @@ This can be overridden by using the `-i` flag to specify a particular Docker ima
 ### Sample Singularity usage
 
 ```
-$ nibabies-wrapper singularity /path/to/data /path/to/output participant --age-months 12 -i nibabies-21.0.0.sif --fs-license-file /usr/freesurfer/license.txt
+$ nibabies-wrapper singularity /path/to/data /path/to/output participant -i nibabies-23.0.0.sif --fs-license-file /usr/freesurfer/license.txt
 
 RUNNING: singularity run --cleanenv -B /path/to/data:/data:ro \
 -B /path/to/output:/out -B /usr/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
-nibabies-21.0.0.sif /data /out participant --age-months 12
+nibabies-23.0.0.sif /data /out participant
 ...
 ```