From 3405f707576464c4e692fedee7e7d30c91121cc2 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 24 Mar 2026 10:59:49 -0400 Subject: [PATCH] Update documentation. I tasked Cursor with synchronizing the documentation across ModelArray, ModelArrayIO, and ConFixel. --- README.md | 74 ++++++------------------------------------------------- 1 file changed, 7 insertions(+), 67 deletions(-) diff --git a/README.md b/README.md index 4249638..cfb152b 100644 --- a/README.md +++ b/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). -

- -![Overview](overview_structure.png) - -

- -`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.