Update readme

README.md

@@ -1,4 +1,4 @@
-# pyvista-ftetwild-pipeline
+# mri2mesh
 
 This repository contains a pipeline to generate surfaces from voxelized data using `scikit-image` and `pyvista`. It also contains tools for visualization using `pyvista`.
 
@@ -7,39 +7,39 @@ This repository contains a pipeline to generate surfaces from voxelized data usi
 To install the required packages, run:
 
 ```bash
-python3 -m pip install git+https://github.com/finsberg/pyvista-ftetwild-pipeline.git
+python3 -m pip install git+https://github.com/scientificcomputing/mri2mesh.git
 ```
 
 ## Usage
-The basic using is through the command line using the command `mri2fem`. To see all the options, run:
+The basic using is through the command line using the command `mri2mesh`. To see all the options, run:
 
 ```bash
-mri2fem --help
+mri2mesh --help
 ```
 
 ### Visualization
 Visualization is achieved through the subcommand `viz`. To see all options you can do
 
 ```bash
-mri2fem viz --help
+mri2mesh viz --help
 ```
 
 For example to visualize a nifty file called `T1_synthseg.nii.gz`, run:
 
 ```bash
-mri2fem viz volume-clip -i T1_synthseg.nii.gz
+mri2mesh viz volume-clip -i T1_synthseg.nii.gz
 ```
 which will open up the volume with a clipping plane. To see all the options, run:
 
 ```bash
-mri2fem viz volume-clip --help
+mri2mesh viz volume-clip --help
 ```
 
 ### Surface generation
-To generate a surface from a nifty file, run:
+To generate the parenchyma surface from a nifty file, run:
 
 ```bash
-mri2fem surface -i T1_synthseg.nii.gz
+mri2mesh surface parenchyma -i T1_synthseg.nii.gz
 ```
 
 ## Authors