Update documentation

README.md

@@ -1,71 +1,11 @@
-# ConFixel: Moved to ModelArrayIO
+# ConFixel is deprecated
 
-ConFixel has moved beyond fixels and handles a lot of other modalities.
-It also got optimized!
-[Going forward, ConFixel is now ModelArrayIO.](https://pennlinc.github.io/ModelArrayIO/). 
-This repository will be left here because the URL is in the publication.
+**This repository is archived.** Development continues as [**ModelArrayIO**](https://github.com/PennLINC/ModelArrayIO).
 
+Use [**ModelArrayIO**](https://github.com/PennLINC/ModelArrayIO#installation) for installation, walkthroughs, and command-line tools (`confixel`, `convoxel`, `concifti`, `fixelstats_write`, `volumestats_write`, `ciftistats_write`). The companion R package [**ModelArray**](https://pennlinc.github.io/ModelArray/) performs voxel-, fixel-, and greyordinate-wise statistics on HDF5 data produced by ModelArrayIO.
 
-`ConFixel` is companion converter software for [ModelArray](https://pennlinc.github.io/ModelArray/) for converting data back and forth from the HDF5 file format.
+- **Installation (ModelArray + ModelArrayIO):** [ModelArray vignette — Installation](https://pennlinc.github.io/ModelArray/articles/installations.html)
+- **Combined walkthrough:** [ModelArray + ModelArrayIO example](https://pennlinc.github.io/ModelArray/articles/walkthrough.html)
+- **Publication:** If you need to cite work that referenced this repository, see the [ModelArray NeuroImage paper](https://doi.org/10.1016/j.neuroimage.2023.120037).
 
-<p align="center">
-
-![Overview](overview_structure.png)
-
-</p>
-
-`ConFixel` software includes three converters: `ConFixel` for fixel-wise data (`.mif`), `ConVoxel` for voxel-wise data (NIfTI) and `ConCIFTI` for CIFTI-2 dscalar files. Each converter converts between the original image format and the HDF5 file format (`.h5`) that ModelArray uses.
-
-Below lists the commands in each converter. After [installation](#installation), these commands can be directly called in a terminal console.
-
-* `ConFixel` converter for fixel-wise data (MRtrix image format `.mif`):
-    * `.mif` --> `.h5`: command `confixel`
-    * `.h5` --> `.mif`: command `fixelstats_write`
-* `ConVoxel` converter for voxel-wise data (NIfTI):
-    * NIfTI --> `.h5`: command `convoxel`
-    * `.h5` --> NIfTI: command `volumestats_write`
-* `ConCIFTI` converter for greyordinate-wise data (CIFTI-2):
-    * CIFTI-2 --> `.h5`: command `concifti`
-    * `.h5` --> CIFTI-2: command `ciftistats_write`
-
-## Installation
-### Install dependent software MRtrix (only required for fixel-wise data `.mif`)
-When converting fixel-wise data's format (`.mif`), converter `ConFixel` uses function `mrconvert` from MRtrix, so please make sure MRtrix has been installed. If it's not installed yet, please refer to [MRtrix's webpage](https://www.mrtrix.org/download/) for how to install it. Type `mrview` in the terminal to check whether MRtrix installation is successful.
-
-If your input data is voxel-wise data or CIFTI (greyordinate-wise) data, you can skip this step.
-
-### Install `ConFixel` software
-Before installing ConFixel software, you may want to create a conda environment  - see [here](https://pennlinc.github.io/ModelArray/articles/installations.html) for more. If you installed MRtrix in a conda environment, you can directly install ConFixel software in that environment.
-
-You can install `ConFixel` software from `GitHub`:
-
-``` console
-git clone https://github.com/PennLINC/ConFixel.git
-cd ConFixel
-pip install .   # build via pyproject.toml
-```
-
-If you are a developer, and if there is any update in the source code locally, you may update the installation with an editable install:
-
-``` console
-# From the repository root
-pip install -e .
-```
-
-Alternatively, if you have `hatch` installed, you can build wheels/sdist locally:
-
-``` console
-hatch build
-pip install dist/*.whl
-```
-
-## How to use
-We provide [walkthrough for how to use `ConFixel` for fixel-wise data](notebooks/walkthrough_fixel-wise_data.md), and [walkthrough for `ConVoxel` for voxel-wise data](notebooks/walkthrough_voxel-wise_data.md).
-
-As `ConFixel` software is usually used together with [ModelArray](https://pennlinc.github.io/ModelArray/), we also provide [a combined walkthrough](https://pennlinc.github.io/ModelArray/articles/walkthrough.html) of ConFixel + ModelArray with example fixel-wise data.
-
-You can also refer to `--help` for additional information:
-``` console
-confixel --help
-```
-You can replace `confixel` with other commands in ConFixel.
+This repo is retained for history and publication links only; do not open new issues or PRs here—use [ModelArrayIO](https://github.com/PennLINC/ModelArrayIO/issues) or [ModelArray](https://github.com/PennLINC/ModelArray/issues) as appropriate.