update doc

README.md

@@ -7,8 +7,9 @@
 GLMsingle is a toolbox for obtaining accurate single-trial estimates
 in fMRI time-series data. We provide both MATLAB and Python implementations. 
 
-**The GLMsingle preprint, which describes the technique in detail, 
-is available on bioRxiv (https://www.biorxiv.org/content/10.1101/2022.01.31.478431v1).**
+GLMsingle is detailed in the following paper:
+
+**[Prince, J.S., Charest, I., Kurzawski, J.W., Pyles, J.A., Tarr, M., Kay, K.N. Improving the accuracy of single-trial fMRI response estimates using GLMsingle. *eLife* (2022).](https://doi.org/10.7554/eLife.77599)**
 
 For additional documentation and FAQ on GLMsingle,
 please see: **https://glmsingle.readthedocs.io**
@@ -43,12 +44,14 @@ To install:
 pip install git+https://github.com/cvnlab/GLMsingle.git
 ```
 
-Running the demos requires:
+Running the example scripts requires:
 
-- jupyter notebook or jupyter lab.
+- installing jupyter notebook or jupyter lab
+- cloning the GLMsingle repository in order to get the example scripts located in `examples`:
 
 ```bash
 pip install jupyterlab
+git clone --recurse-submodules https://github.com/cvnlab/GLMsingle.git
 ```
 
 Code dependencies: see [requirements.txt](./requirements.txt)
@@ -68,21 +71,22 @@ We provide a number of example scripts that demonstrate usage of GLMsingle. You
 
 (MATLAB Example 2 - block design) https://htmlpreview.github.io/?https://github.com/kendrickkay/GLMsingle/blob/main/matlab/examples/example2preview/example2.html
 
-If you would like to run these example scripts, the Python versions are available in `/GLMsingle/examples`, and the MATLAB versions are available in `/GLMsingle/matlab/examples`. Each notebook contains a full walkthrough of the process of loading an example dataset and design matrix, estimating neural responses using GLMsingle, estimating the reliability of responses at each voxel, and comparing those achieved via GLMsingle to those achieved using a baseline GLM.
+If you would like to run these example scripts, the Python versions are available in `/GLMsingle/examples`, and the MATLAB versions are available in `/GLMsingle/matlab/examples`.
+
+The first two notebooks contain a full walkthrough of the process of loading an example dataset and design matrix, estimating neural responses using GLMsingle, estimating the reliability of responses at each voxel, and comparing those achieved via GLMsingle to those achieved using a baseline GLM.
+
+The remaining notebooks illustrate a number of other analyses that may be useful for the user to browse.
 
 ## Additional information
 
 Terms of use: This content is licensed under a BSD 3-Clause License.
 
 If you use GLMsingle in your research, please cite the following paper:
 
-* [Prince, J.S., Charest, I., Kurzawski, J.W., Pyles, J.A., Tarr, M.J., Kay, K.N. GLMsingle: a toolbox for improving single-trial fMRI response estimates. bioRxiv (2022).](https://www.biorxiv.org/content/10.1101/2022.01.31.478431v1)
-
-## Contributing
-
-If you want to contribute to GLMsingle see the [contributing](./CONTRIBUTING.md) documentation to help you know what is where and how to set things up.
+* [Prince, J.S., Charest, I., Kurzawski, J.W., Pyles, J.A., Tarr, M., Kay, K.N. Improving the accuracy of single-trial fMRI response estimates using GLMsingle. *eLife* (2022).](https://doi.org/10.7554/eLife.77599)
 
 ## Change history
 
+* 2022/11/28 - Version 1.1 of GLMsingle is now released. A git tag has been added to the repo. This version corresponds to what is described in the Prince et al. 2022 paper.
 * 2021/10/12 - Version 1.0 of GLMsingle is now released. A git tag has been added to the repo.
 * 2021/05/21 - The core code is complete, but is in "beta" and we are generating tutorial examples of usage. The initial 1.0 release should be forthcoming.