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FAQ: add entry about demeaning in RSA

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nno committed Nov 3, 2017
1 parent 440d1e5 commit bd4620bc031aa6c7b1be3692de5620263b7fd86f
Showing with 28 additions and 1 deletion.
  1. +9 −0 doc/source/faq.rst
  2. +10 −0 doc/source/references.bib
  3. +9 −1 mvpa/cosmo_target_dsm_corr_measure.m
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@@ -1412,6 +1412,15 @@ Yes, although it requires a bit of extra work. You would run :ref:`cosmo_montec
ds_tfce.samples=combined_z;
cosmo_check_dataset(ds_tfce)
Why should I consider re-meaning when doing representational similarity analysis (RSA)?
---------------------------------------------------------------------------------------
'In the * :ref:`cosmo_target_dsm_corr_measure` *documentation it is recommended to subtract the mean activity pattern first. Why is this recommended?'
This is explained well in :cite:`DK17`:
`Activity estimates commonly co-vary together across fMRI imaging runs, because all activity estimates within a partition are measured relative to the same resting baseline. This positive correlation can be reduced by subtracting, within each partition, the mean activity pattern (across conditions) from each activity pattern. This makes the mean of each measurement channel (across condition) zero and thus centers the ensemble of points in activity-pattern space that is centered on the origin.'
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@@ -265,6 +265,16 @@ @article{KOP16
publisher={Soc Neuroscience}
}
@article{DK17,
title={Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis},
author={Diedrichsen, J{\"o}rn and Kriegeskorte, Nikolaus},
journal={PLoS computational biology},
volume={13},
number={4},
pages={e1005508},
year={2017},
publisher={Public Library of Science}
}
@@ -52,7 +52,9 @@
% computing the pairwise distances for all samples in ds.
% This is generally recommended but is not the default in
% order to avoid breaking behavaiour from earlier
% versions.
% versions. For a rationale why this is recommendable, see
% the Diedrichsen & Kriegeskorte article (below in
% references)
% Default: false
%
% Output:
@@ -148,6 +150,12 @@
% dataset's samples, are ignored. Masking is done prior to z-score
% normalization.
%
% Reference:
% - Diedrichsen, J., & Kriegeskorte, N. (2017). Representational
% models: A common framework for understanding encoding,
% pattern-component, and representational-similarity analysis.
% PLoS computational biology, 13(4), e1005508.
%
%
% # For CoSMoMVPA's copyright information and license terms, #
% # see the COPYING file distributed with CoSMoMVPA. #

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