DOC improve the description of the voxelwise modeling framework

Author: TomDLT

README.rst

@@ -11,9 +11,10 @@ Tutorials
 =========
 
 This repository contains tutorials describing how to use the voxelwise modeling
-framework. Voxelwise modeling is a framework to perform functional magnetic
-resonance imaging (fMRI) data analysis, fitting encoding models at the voxel
-level.
+framework. `Voxelwise modeling
+<https://gallantlab.github.io/voxelwise_tutorials/voxelwise_modeling.html>`_ is
+a framework to perform functional magnetic resonance imaging (fMRI) data
+analysis, fitting encoding models at the voxel level.
 
 To explore these tutorials, one can:
 
@@ -100,7 +101,7 @@ If you use one of our packages in your work (``voxelwise_tutorials`` [1]_,
 ``himalaya`` [2]_, ``pycortex`` [3]_, or ``pymoten`` [4]_), please cite the
 corresponding publications:
 
-.. [1] Dupré La Tour, T., Visconti di Oleggio Castello, M., & Gallant, J. L. (2022).
+.. [1] Dupré La Tour, T., Visconti di Oleggio Castello, M., & Gallant, J. L. (2023).
    Voxelwise modeling tutorials: an encoding model approach to functional MRI analysis.
    *In preparation*.
 

doc/conf.py

@@ -70,7 +70,7 @@
 
 # General information about the project.
 project = u'Voxelwise modeling tutorials'
-copyright = u'2020, Gallant lab'
+copyright = u'2023, Gallant lab'
 author = u'Gallant lab'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -87,7 +87,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

doc/index.rst

@@ -38,26 +38,22 @@ Navigation
 .. toctree::
    :includehidden:
    :maxdepth: 1
-   
-    
-   _auto_examples/index
-
-.. toctree::
-   :maxdepth: 1
 
-   voxelwise_package
+   _auto_examples/index
 
 .. toctree::
    :maxdepth: 1
 
    voxelwise_modeling
+   voxelwise_package
+   references
 
 Cite as
 -------
 
 If you use one of our packages in your work (``voxelwise_tutorials``
-:ref:`[13]<dup2022b>`, ``himalaya`` :ref:`[14]<dup2022>`, ``pycortex``
-:ref:`[15]<gao2015>`, or ``pymoten`` :ref:`[16]<nun2021>`), please cite the
+:ref:`[p1]<dup2023>`, ``himalaya`` :ref:`[p2]<dup2022>`, ``pycortex``
+:ref:`[p3]<gao2015>`, or ``pymoten`` :ref:`[p4]<nun2021>`), please cite the
 corresponding publications.
 
 If you use one of our public datasets in your work (vim-2

doc/references.rst

@@ -0,0 +1,147 @@
+References
+==========
+
+Voxelwise modeling (VM) is a framework to perform functional magnetic resonance
+imaging (fMRI) data analysis. Over the years, VM has led to many high profile
+publications :ref:`[1]<kay2008>` :ref:`[2]<nas2009>` :ref:`[3]<nis2011>`
+:ref:`[4]<hut2012>` :ref:`[5]<cuk2013>` :ref:`[6]<cuk2013b>`
+:ref:`[7]<sta2013>` :ref:`[8]<hut2016>` :ref:`[9]<deh2017>`
+:ref:`[10]<les2019>` :ref:`[11]<den2019>` :ref:`[12]<nun2019>`
+:ref:`[13]<pop2021>` :ref:`[14]<leb2021>` :ref:`[15]<dup2022>`.
+
+
+.. _kay2008:
+
+[1] Kay, K. N., Naselaris, T., Prenger, R. J., & Gallant, J. L. (2008).
+    Identifying natural images from human brain activity.
+    Nature, 452(7185), 352-355.
+
+.. _nas2009:
+
+[2] Naselaris, T., Prenger, R. J., Kay, K. N., Oliver, M., & Gallant, J. L. (2009).
+    Bayesian reconstruction of natural images from human brain activity.
+    Neuron, 63(6), 902-915.
+
+.. _nis2011:
+
+[3] 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.
+
+.. _hut2012:
+
+[4] Huth, A. 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.
+
+.. _cuk2013:
+
+[5] Çukur, T., Nishimoto, S., Huth, A. G., & Gallant, J. L. (2013).
+    Attention during natural vision warps semantic representation across the human brain.
+    Nature neuroscience, 16(6), 763-770.
+
+.. _cuk2013b:
+
+[6] Çukur, T., Huth, A. G., Nishimoto, S., & Gallant, J. L. (2013).
+    Functional subdomains within human FFA.
+    Journal of Neuroscience, 33(42), 16748-16766.
+
+.. _sta2013:
+
+[7] Stansbury, D. E., Naselaris, T., & Gallant, J. L. (2013).
+    Natural scene statistics account for the representation of scene categories
+    in human visual cortex.
+    Neuron, 79(5), 1025-1034
+
+.. _hut2016:
+
+[8] Huth, A. G., De Heer, W. A., Griffiths, T. L., Theunissen, F. E., & Gallant, J. L. (2016).
+    Natural speech reveals the semantic maps that tile human cerebral cortex.
+    Nature, 532(7600), 453-458.
+
+.. _deh2017:
+
+[9] de Heer, W. A., Huth, A. G., Griffiths, T. L., Gallant, J. L., & Theunissen, F. E. (2017).
+    The hierarchical cortical organization of human speech processing.
+    Journal of Neuroscience, 37(27), 6539-6557.
+
+.. _les2019:
+
+[10] Lescroart, M. D., & Gallant, J. L. (2019).
+    Human scene-selective areas represent 3D configurations of surfaces.
+    Neuron, 101(1), 178-192.
+
+.. _den2019:
+
+[11] Deniz, F., Nunez-Elizalde, A. O., Huth, A. G., & Gallant, J. L. (2019).
+    The representation of semantic information across human cerebral cortex
+    during listening versus reading is invariant to stimulus modality.
+    Journal of Neuroscience, 39(39), 7722-7736.
+
+.. _nun2019:
+
+[12] Nunez-Elizalde, A. O., Huth, A. G., & Gallant, J. L. (2019).
+    Voxelwise encoding models with non-spherical multivariate normal priors.
+    Neuroimage, 197, 482-492.
+
+.. _pop2021:
+
+[13] Popham, S. F., Huth, A. G., Bilenko, N. Y., Deniz, F., Gao, J. S.,
+    Nunez-Elizalde, A. O., & Gallant, J. L. (2021).
+    Visual and linguistic semantic representations are aligned at the border of
+    human visual cortex.
+    Nature Neuroscience, 24(11), 1628-1636.
+
+.. _leb2021:
+
+[14] LeBel, A., Jain, S., & Huth, A. G. (2021).
+    Voxelwise encoding models show that cerebellar language representations are
+    highly conceptual.
+    Journal of Neuroscience, 41(50), 10341-10355.
+
+.. _dup2022:
+
+[15] Dupré La Tour, T., Eickenberg, M., Nunez-Elizalde, A.O., & Gallant, J. L. (2022).
+    Feature-space selection with banded ridge regression.
+    NeuroImage. https://doi.org/10.1016/j.neuroimage.2022.119728
+
+Datasets
+--------
+
+.. _nis2011data:
+
+[3b] Nishimoto, S., Vu, A. T., Naselaris, T., Benjamini, Y., Yu, B., & Gallant, J. L. (2014).
+    Gallant Lab Natural Movie 4T fMRI Data.
+    CRCNS.org. http://dx.doi.org/10.6080/K00Z715X
+
+.. _hut2012data:
+
+[4b] Huth, A. G., Nishimoto, S., Vu, A. T., Dupré la Tour, T., & Gallant, J. L. (2022).
+    Gallant Lab Natural Short Clips 3T fMRI Data.
+    GIN. http://dx.doi.org/10.12751/g-node.vy1zjd
+
+Packages
+--------
+
+.. _dup2023:
+
+[p1] Dupré La Tour, T., Visconti di Oleggio Castello, M., & Gallant, J. L. (2023).
+   Voxelwise modeling tutorials: an encoding model approach to functional MRI analysis.
+   *In preparation*.
+
+[p2] Dupré La Tour, T., Eickenberg, M., Nunez-Elizalde, A.O., & Gallant, J. L. (2022).
+    Feature-space selection with banded ridge regression.
+    NeuroImage. https://doi.org/10.1016/j.neuroimage.2022.119728
+
+.. _gao2015:
+
+[p3] Gao, J. S., Huth, A. G., Lescroart, M. D., & Gallant, J. L. (2015).
+    Pycortex: an interactive surface visualizer for fMRI.
+    Frontiers in Neuroinformatics, 23. https://doi.org/10.3389/fninf.2015.00023
+
+.. _nun2021:
+
+[p4] Nunez-Elizalde, A.O., Deniz, F., Dupré la Tour, T., Visconti di Oleggio Castello, M., and Gallant, J.L. (2021).
+    pymoten: scientific python package for computing motion energy features from video.
+    Zenodo. https://doi.org/10.5281/zenodo.6349625