Small doc changes

README.md

@@ -1,16 +1,16 @@
 # Fetal CP Surface Extraction
 
-[![Version](https://img.shields.io/docker/v/fnndsc/pl-fetal-cp-surface-extract?sort=semver)](https://hub.docker.com/r/fnndsc/pl-fetal-cp-surface-extract)
-[![MIT License](https://img.shields.io/github/license/fnndsc/pl-fetal-cp-surface-extract)](https://github.com/FNNDSC/pl-fetal-cp-surface-extract/blob/main/LICENSE)
-[![ci](https://github.com/FNNDSC/pl-fetal-cp-surface-extract/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-fetal-cp-surface-extract/actions/workflows/ci.yml)
+[![Version](https://img.shields.io/docker/v/fnndsc/pl-fetal-surface-extract?sort=semver)](https://hub.docker.com/r/fnndsc/pl-fetal-surface-extract)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-fetal-surface-extract)](https://github.com/FNNDSC/pl-fetal-surface-extract/blob/main/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-fetal-surface-extract/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-fetal-surface-extract/actions/workflows/ci.yml)
 
 Fetal brain cortical plate surface extraction using CIVET marching-cubes (`sphere_mesh`).
 
 ![Figure](docs/fig.png)
 
 ## Abstract
 
-`pl-fetal-cp-surface-extract` consumes binary volumetric `.mnc` brain masks to produce
+`pl-fetal-surface-extract` consumes binary volumetric `.mnc` brain masks to produce
 surfaces as `.obj` files with standard connectivity (81,920 triangles). This program is
 suitable for targeting the **inner cortical plate** surface (gray-white matter boundary)
 of high-quality human fetal brain MRI segmentation for subjects between 23-35 gestational
@@ -21,29 +21,29 @@ weeks of age.
 Polygonal surface mesh representations of brain hemispheres are useful for measuring cortical
 thickness, image registration, and quantitative regional analysis.
 
-## Marching Cubes
+## Surface Extraction Algorithm
+
+1. Preprocess mask using `mincmorph` to fill in disconnected voxels (improve mask quality)
+2. Marching-cubes -> spherical topology surface mesh with unknown number of triangles
+3. Calculate distance error
+4. _If_ maximum distance error is too large, _then_ redo marching-cubes with subsampling
+5. Sphere-to-sphere interpolation -> resample mesh to standard connectivity of 81,920 triangles, preserving morphology
+6. Calculate smoothness error
+7. Run `adapt_object_mesh` to achieve desired smoothness. Number of iterations is predicted by a regression
+
+### Marching Cubes
 
 We have evaluated two implementations of marching-cubes:
 
-- [scikit-image](https://github.com/FNNDSC/pl-fetal-cp-surface-extract)
+- [scikit-image](https://github.com/FNNDSC/pl-fetal-surface-extract)
 - [CIVET](https://github.com/FNNDSC/ep-sphere_mesh)
 
 We found that CIVET's implementation of the marching-cubes algorithm, `sphere_mesh`, is
 [more accurate](docs/compare_civet_skimage.md)
 than scikit-image's implementation, which requires FWHM blurring of the volume.
 Moreover, `sphere_mesh` guarantees a spherical topology.
 
-## Surface Extraction Algorithm
-
-1. Preprocess mask using `mincmorph` to fill in disconnected voxels (improve mask quality)
-2. Marching-cubes -> spherical topology surface mesh with unknown number of triangles
-3. Calculate distance error
-4. _If_ maximum distance error is too large, _then_ redo marching-cubes with subsampling
-5. Sphere-to-sphere interpolation -> resample mesh to standard connectivity of 81,920 triangles, preserving morphology
-6. Calculate smoothness error
-7. Run `adapt_object_mesh` to achieve desired smoothness. Number of iterations is predicted by a regression model
-
-### Estimation of: How much smoothing?
+### How much Smoothing? Estimation
 
 We developed a model which predicts the number of `adapt_object_mesh` smoothing iterations necessary, given a desired smoothness error threshold.
 The model was created from the experiment described here:
@@ -56,7 +56,7 @@ The model was created from the experiment described here:
 1. https://github.com/FNNDSC/ep-premc-mincmorph
 2. https://github.com/FNNDSC/pl-nums2mask
 3. https://github.com/FNNDSC/pl-subdiv-minc TODO
-4. pl-fetal-cp-surface-extract
+4. pl-fetal-surface-extract
 5. pl-extracted-surface-asp TODO
 
 <!--
@@ -68,10 +68,10 @@ without the extra step the accuracy is nonetheless sufficient.
 
 ## Installation
 
-`pl-fetal-cp-surface-extract` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
+`pl-fetal-surface-extract` is a _[ChRIS](https://chrisproject.org/) plugin_, meaning it can
 run from either within _ChRIS_ or the command-line.
 
-[![Get it from chrisstore.co](https://raw.githubusercontent.com/FNNDSC/ChRIS_store_ui/963938c241636e4c3dc4753ee1327f56cb82d8b5/src/assets/public/badges/light.svg)](https://chrisstore.co/plugin/pl-fetal-cp-surface-extract)
+[![Get it from chrisstore.co](https://raw.githubusercontent.com/FNNDSC/ChRIS_store_ui/963938c241636e4c3dc4753ee1327f56cb82d8b5/src/assets/public/badges/light.svg)](https://chrisstore.co/plugin/pl-fetal-surface-extract)
 
 ## Usage
 
@@ -99,31 +99,31 @@ values shouldn't do any harm, and would help compensate for larger brain sizes.
 
 Copy input mask file to output directory.
 
-`--keep-mask` is a workaround for using `pl-fetal-cp-surface-extract` as part of a
+`--keep-mask` is a workaround for using `pl-fetal-surface-extract` as part of a
 _ChRIS_ pipeline. It eliminates the need for an extra _ts_ plugin step.
 
 ## Local Usage
 
 To get started with local command-line usage, use [Apptainer](https://apptainer.org/)
-to run `pl-fetal-cp-surface-extract` as a container:
+to run `pl-fetal-surface-extract` as a container:
 
 ```shell
-apptainer exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp input/ output/
+apptainer exec docker://fnndsc/pl-fetal-surface-extract extract_cp input/ output/
 ```
 
 To print its available options, run:
 
 ```shell
-apptainer exec docker://fnndsc/pl-fetal-cp-surface-extract extract_cp --help
+apptainer exec docker://fnndsc/pl-fetal-surface-extract extract_cp --help
 ```
 
 ## Suggested Software
 
-### Before `pl-fetal-cp-surface-extract`
+### Before `pl-fetal-surface-extract`
 
 - [`pl-nums2mask`](https://chrisstore.co/plugin/pl-nums2mask): create input masks
 
-### After `pl-fetal-cp-surface-extract`
+### After `pl-fetal-surface-extract`
 
 - [`pl-surfdisterr`](https://chrisstore.co/plugin/pl-surfdisterr): QC
 - [`pl-smoothness-error`](https://chrisstore.co/plugin/pl-smoothness-error): QC
@@ -137,7 +137,7 @@ Instructions for developers.
 Build a local container image:
 
 ```shell
-docker build -t localhost/fnndsc/pl-fetal-cp-surface-extract .
+docker build -t localhost/fnndsc/pl-fetal-surface-extract .
 ```
 
 ### Get JSON Representation
@@ -146,7 +146,7 @@ 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-fetal-cp-surface-extract chris_plugin_info > chris_plugin_info.json
+docker run --rm localhost/fnndsc/pl-fetal-surface-extract chris_plugin_info > chris_plugin_info.json
 ```
 
 ### Local Test Run
@@ -157,5 +157,5 @@ Mount the source code `extract_cp.py` into a container to test changes without r
 docker run --rm -it --userns=host -u $(id -u):$(id -g) \
     -v $PWD/extract_cp:/opt/conda/lib/python3.10/site-packages/extract_cp:ro \
     -v $PWD/in:/incoming:ro -v $PWD/out:/outgoing:rw -w /outgoing \
-    localhost/fnndsc/pl-fetal-cp-surface-extract extract_cp /incoming /outgoing
+    localhost/fnndsc/pl-fetal-surface-extract extract_cp /incoming /outgoing
 ```

docs/compare_civet_skimage.md

@@ -1,5 +1,5 @@
 Brief comparison of marching-cubes implementations between
-[scikit-image](https://github.com/FNNDSC/pl-fetal-cp-surface-extract)
+[scikit-image](https://github.com/FNNDSC/pl-fetal-surface-extract)
 and [CIVET](https://github.com/FNNDSC/ep-sphere_mesh).
 
 Cost function is mean

setup.py

@@ -6,7 +6,7 @@
     description='Fetal brain MRI CP surface extraction using CIVET marching-cubes',
     author='Jennings Zhang',
     author_email='Jennings.Zhang@childrens.harvard.edu',
-    url='https://github.com/FNNDSC/pl-fetal-cp-surface-extract',
+    url='https://github.com/FNNDSC/pl-fetal-surface-extract',
     packages=find_packages(exclude=['tests']),
     install_requires=['chris_plugin', 'loguru', 'pycivet', 'pybicpl', 'numpy'],
     license='MIT',