diff --git a/README.md b/README.md
index a5b330a1..27a99472 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,3 @@
-
-
# Advanced Normalization Tools in Python
@@ -7,7 +5,7 @@
- 
+
@@ -18,7 +16,6 @@
[](https://mybinder.org/v2/gh/stnava/ANTsPyDocker/master)
[](https://pubmed.ncbi.nlm.nih.gov/33907199/)
-
## About ANTsPy
Search [ANTsPy documentation at read the docs.](https://antspyx.readthedocs.io/en/latest/?badge=latest)
@@ -38,19 +35,20 @@ scratch - see [C++ Wrap Guide](tutorials/UsingITK.md) for a succinct tutorial.
If you want to contribute to ANTsPy or simply want to learn about the package architecture
and wrapping process, please read the extensive [contributors guide](CONTRIBUTING.md).
-If you have any questions or feature requests, feel free to open an issue or email Nick (ncullen at pennmedicine dot upenn dot edu).
+If you have any questions or feature requests, feel free to open an issue.
## Installation
### NOTE: old pip wheels will be deleted!!!
-we dont have the quota on pypi to support more than one or two prior releases. if you care about this: (1) open a pypi issue requesting more quota for this project; (2) propose another alternative.
+we dont have the quota on pypi to support more than one or two prior releases. if you care about this: (1) open a pypi issue requesting more quota for this project; (2) propose another alternative.
We recommend that users install the latest pre-compiled binaries, which takes ~1 minute. Note
that ANTsPy is not currently tested for Python 2.7 support.
Copy the following command and paste it into your bash terminal:
For MacOS and Linux:
+
```bash
pip install antspyx
```
@@ -64,34 +62,34 @@ git clone https://github.com/ANTsX/ANTsPy
cd ANTsPy
python3 setup.py install
```
+
or see below for an alternative strategy using `pip`. If you want more detailed instructions
on compiling ANTsPy from source, you can read the
[installation tutorial](https://github.com/ANTsX/ANTsPy/blob/master/tutorials/InstallingANTsPy.md).
-
### Installing older versions
We cannot store the entire history of releases because storage space on `pip` is limited.
if you need an older release, you can check the [Github Releases page](https://github.com/ANTsX/ANTsPy/releases) or
-build from source.
+build from source.
Try something like:
```bash
pip install 'antspyx @ git+https://github.com/ANTsX/ANTsPy@v0.3.2'
```
-which will attempt to build from source (requires a machine with developer tools).
-
+which will attempt to build from source (requires a machine with developer tools).
### Recent wheels
Non-release commits have wheels built automatically, which are available for download for a limited period.
-Look under the [Actions tab](https://github.com/ANTsX/ANTsPy/actions). Then click on the commit for the software version you want.
+Look under the [Actions tab](https://github.com/ANTsX/ANTsPy/actions). Then click on the commit for the software version you want.
Recent commits will have wheels stored as "artifacts".
we build wheels locally like this:
+
```
rm -r -f build/ antspymm.egg-info/ dist/
python3 setup.py sdist bdist_wheel
@@ -103,13 +101,14 @@ pipx run twine upload dist/*
Available on [Docker Hub](https://hub.docker.com/repository/docker/antsx/antspy). To build
ANTsPy docker images, see the (installation tutorial)(https://github.com/ANTsX/ANTsPy/blob/master/tutorials/InstallingANTsPy.md#docker-installation).
-------------------------------------------------------------------------------
+---
## ANTsR Comparison
Here is a quick example to show the similarity with ANTsR:
ANTsR code:
+
```R
library(ANTsR)
img <- antsImageRead(getANTsRData("r16"))
@@ -119,6 +118,7 @@ segs1 <- atropos(a=img, m='[0.2,1x1]', c='[2,0]', i='kmeans[3]', x=mask )
```
ANTsPy code:
+
```python
from ants import atropos, get_ants_data, image_read, resample_image, get_mask
img = image_read(get_ants_data("r16"))