Update README.md

README.md

@@ -5,12 +5,19 @@
 [![ci](https://github.com/FNNDSC/pl-bestsurfreg-surface-resample/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-bestsurfreg-surface-resample/actions/workflows/ci.yml)
 
 `pl-bestsurfreg-surface-resample` is a [_ChRIS_](https://chrisproject.org/)
-_ds_ plugin which takes in ...  as input files and
-creates ... as output files.
+_ds_ plugin which does surface registration using MNI/CIVET tools.
+The inputs are MNI `.obj` surfaces of either the left or right brain hemisphere.
+For each surface, the registered vertex-wise data is produced as a `.txt` file,
+as well as the intermediate `.sm` registration map file.
 
-## Abstract
+In its default configuration, it uses the average 29 gestational age
+fetal brain template of the [Im Lab](https://research.childrenshospital.org/neuroim/)
+to register a mask of the medial cut.
 
-...
+![before](img/before.png)
+![after](img/after.png)
+
+Figure: (Left) mask does not cover medial cut. (Right) mask is registered to cover the medial cut.
 
 ## Installation
 
@@ -25,85 +32,11 @@ To get started with local command-line usage, use [Apptainer](https://apptainer.
 (a.k.a. Singularity) to run `pl-bestsurfreg-surface-resample` as a container:
 
 ```shell
-apptainer exec docker://fnndsc/pl-bestsurfreg-surface-resample bsr2 [--args values...] input/ output/
+apptainer exec docker://fnndsc/pl-bestsurfreg-surface-resample bsrr [--args values...] input/ output/
 ```
 
 To print its available options, run:
 
 ```shell
-apptainer exec docker://fnndsc/pl-bestsurfreg-surface-resample bsr2 --help
-```
-
-## Examples
-
-`bsr2` requires two positional arguments: a directory containing
-input data, and a directory where to create output data.
-First, create the input directory and move input data into it.
-
-```shell
-mkdir incoming/ outgoing/
-mv some.dat other.dat incoming/
-apptainer exec docker://fnndsc/pl-bestsurfreg-surface-resample:latest bsr2 [--args] incoming/ outgoing/
-```
-
-## Development
-
-Instructions for developers.
-
-### Building
-
-Build a local container image:
-
-```shell
-docker build -t localhost/fnndsc/pl-bestsurfreg-surface-resample .
-```
-
-### Running
-
-Mount the source code `bsr2.py` into a container to try out changes without rebuild.
-
-```shell
-docker run --rm -it --userns=host -u $(id -u):$(id -g) \
-    -v $PWD/bsr2.py:/usr/local/lib/python3.11/site-packages/bsr2.py:ro \
-    -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-bestsurfreg-surface-resample bsr2 /incoming /outgoing
-```
-
-### Testing
-
-Run unit tests using `pytest`.
-It's recommended to rebuild the image to ensure that sources are up-to-date.
-Use the option `--build-arg extras_require=dev` to install extra dependencies for testing.
-
-```shell
-docker build -t localhost/fnndsc/pl-bestsurfreg-surface-resample:dev --build-arg extras_require=dev .
-docker run --rm -it localhost/fnndsc/pl-bestsurfreg-surface-resample:dev pytest
+apptainer exec docker://fnndsc/pl-bestsurfreg-surface-resample bsrr --help
 ```
-
-## Release
-
-Steps for release can be automated by [Github Actions](.github/workflows/ci.yml).
-This section is about how to do those steps manually.
-
-### Increase Version Number
-
-Increase the version number in `setup.py` and commit this file.
-
-### Push Container Image
-
-Build and push an image tagged by the version. For example, for version `1.2.3`:
-
-```
-docker build -t docker.io/fnndsc/pl-bestsurfreg-surface-resample:1.2.3 .
-docker push docker.io/fnndsc/pl-bestsurfreg-surface-resample:1.2.3
-```
-
-### Get JSON Representation
-
-Run [`chris_plugin_info`](https://github.com/FNNDSC/chris_plugin#usage)
-to produce a JSON description of this plugin, which can be uploaded to a _ChRIS Store_.
-
-```shell
-docker run --rm localhost/fnndsc/pl-bestsurfreg-surface-resample:dev chris_plugin_info > chris_plugin_info.json
-```
-