DOC improve README's 'How to get started'

README.md

@@ -2,34 +2,90 @@
 
 ## Summary
 
-This data set contains BOLD fMRI responses in human subjects viewing a set of
+This dataset contains BOLD fMRI responses in human subjects viewing a set of
 natural short movie clips. The functional data were collected in five subjects,
 in three sessions over three separate days for each subject. Details of the
 experiment are described in the original publication [1].
 
-The natural short movie clips used in this dataset are identical to those used
-in a previous experiment described in [2]. However, the functional data is different.
-This data set contains full brain responses recorded every two seconds with a 3T scanner [1].
-The data set described in [2] contains responses from the occipital lobe only,
-recorded every second with a 4T scanner.
+> **[1]** Huth, Alexander G., Nishimoto, S., Vu, A. T., & Gallant, J. L.
+> (2012). A continuous semantic space describes the representation of thousands
+> of object and action categories across the human brain. Neuron, 76(6),
+> 1210-1224. https://dx.doi.org/10.1016/j.neuron.2012.10.014
 
-> **[1]** Huth, Alexander G., Nishimoto, S., Vu, A. T., & Gallant, J. L. (2012).
-A continuous semantic space describes the representation of thousands of object
-and action categories across the human brain. Neuron, 76(6), 1210-1224.
+If you publish any work using the dataset, please cite the original publication
+[1], and cite the dataset [1b] in the following recommended format:
 
-> **[2]** Nishimoto, S., Vu, A. T., Naselaris, T., Benjamini, Y., Yu, B., & Gallant,
-J. L. (2011). Reconstructing visual experiences from brain activity evoked by
-natural movies. Current Biology, 21(19), 1641-1646.
+> **[1b]** Huth, A. G., Nishimoto, S., Vu, A. T., Dupre la Tour, T., & Gallant,
+> J. L. (2022). Gallant Lab Natural Short Clips 3T fMRI Data.
+> https://dx.doi.org/--TBD--
 
-## Cite this dataset
+#### Difference with the "vim-2" dataset
 
-If you publish any work using the data, please cite the original publication [1],
-and cite the dataset in the following recommended format:
+The present dataset uses the same stimuli (natural short movie clips) than a
+previous experiment of the Gallant lab [2], publicly released in CRCNS under
+the name ["vim-2"](https://crcns.org/data-sets/vc/vim-2/) [2b]. Both dataset
+use the same stimuli, but the functional data is different.
 
-> **[3]** Huth, A. G., Nishimoto, S., Vu, A. T., Dupre la Tour, T., & Gallant, J. L. (2022).
-Gallant Lab Natural Short Clips 3T fMRI Data. http://dx.doi.org/--TBD--
+The "shortclips" dataset [1b] contains full brain responses recorded every two
+seconds (2s) with a 3T scanner. The "vim-2" dataset [2b] contains responses
+from the occipital lobe only, recorded every second (1s) with a 4T scanner.
+Contrary to the "shortclips" dataset, the "vim-2" dataset does not provide
+mappers to plot the data on flatten maps of the cortical surface.
 
-## Data files organization
+
+> **[2]** Nishimoto, S., Vu, A. T., Naselaris, T., Benjamini, Y., Yu, B., &
+> Gallant, J. L. (2011). Reconstructing visual experiences from brain activity
+> evoked by natural movies. Current Biology, 21(19), 1641-1646.
+> https://dx.doi.org/10.1016/j.cub.2011.08.031
+
+> **[2b]** Nishimoto, S., Vu, A. T., Naselaris, T., Benjamini, Y., Yu, B., &
+> Gallant, J. L. (2014). Gallant Lab Natural Movie 4T fMRI Data. CRCNS.org.
+> https://dx.doi.org/10.6080/K00Z715X
+
+## How to get started
+
+#### a. With dedicated tutorials
+The preferred way to explore this dataset is through the [voxelwise
+tutorials](https://github.com/gallantlab/voxelwise_tutorials). These tutorials
+includes Python downloading tools, data loaders, plotting utilities, and
+examples of analysis following the original publication [1] [2].
+
+<a href="https://gallantlab.github.io/voxelwise_tutorials/"><img
+src="https://gallantlab.github.io/voxelwise_tutorials/_images/sphx_glr_06_plot_banded_ridge_model_002.png"
+alt="Example" width="600"/></a>
+
+#### b. With git and git-annex
+
+To download the data with [git-annex](https://git-annex.branchable.com/), run
+the commands:
+```bash
+# clone the repository, without the data files
+git clone https://gin.g-node.org/gallantlab/shortclips
+cd shortclips
+# download one file (e.g. features/wordnet.hdf)
+git annex get features/wordnet.hdf --from wasabi
+# download all files 
+git annex get . --from wasabi
+```
+
+To maximize the downloading speed, two remotes are available to download the
+data. The first remote is GIN (`--from origin`), but the bandwidth might be
+limited. The second remote is Wasabi (`--from wasabi`), with a larger
+bandwidth.
+
+To load and plot the data, a basic example script is available in `example.py`.
+For more utilities and examples of analysis, see the dedicated [voxelwise
+tutorials](https://github.com/gallantlab/voxelwise_tutorials).
+
+#### How to get help
+
+The recommended way to ask questions is in the issue tracker on the GitHub page
+https://github.com/gallantlab/voxelwise_tutorials/issues.
+
+
+## Data set content
+
+#### Data file organization
 
 ```text
 features/                    → feature spaces used for voxelwise modeling
@@ -49,12 +105,12 @@ stimuli/                     → natural movie stimuli, for each fMRI run
     ...
     train_11.hdf
 utils/
-    example.py               → Python functions to analyze the data
     wordnet_categories.txt   → names of the wordnet labels
     wordnet_graph.dot        → wordnet graph to plot as in [1]
+example.py                   → Python example to load and plot the data
 ```
 
-## Data format
+#### Data format
 
 All files are hdf5 files, with multiple arrays stored inside.
 The names, shapes, and descriptions of each array are listed below.
@@ -100,27 +156,4 @@ Each file in `stimuli` contains:
         Each training run contains 9000 images total.
         The test run contains 8100 images total.
 ```
-The `utils.py` file contains helpers to load the data in Python.
-
-## How to get started
-
-The `utils` directory contains basic Python helpers to get started with
-the data.
-
-More tutorials on voxelwise modeling using this data set are available at
-https://github.com/gallantlab/voxelwise_tutorials.
-They includes Python downloading tools, data loaders,
-plotting tools, and examples of analysis.
-
 
-<img src="https://gallantlab.github.io/voxelwise_tutorials/_images/sphx_glr_06_plot_banded_ridge_model_002.png" alt="Example" width="600"/>
-
-Note that to get started, you might not need to download all the data. In
-particular, the stimuli data is large, and is already processed into two
-feature spaces to be used in voxelwise modeling.
-
-
-## How to get help
-
-The recommended way to ask questions is in the issue tracker on the GitHub page
-https://github.com/gallantlab/voxelwise_tutorials/issues.