Brainder.

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Some image processing methods implicitly smooth images with an ideal filter. What's the FWHM of the Gaussian filter that produces the most similar degree of smoothing?

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A script to define optimal directions in multishell diffusion MRI and prepare files for different scanners.

Uniform directions for multi-shell diffusion MRI

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We need better phenotypes

We need better phenotypes

Marek, Tervo-Clemmens et al. (2022) suggest that we need much larger sample sizes to investigate associations between common variability in brain structure or function and cognition or psychiatric symptomatology. That is true under the assumption that such associations, for complex, multifactorial cognitive or psychiatric phenotypes, and characteristics accessible with existing imaging methods,…

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How many principal components?

How many principal components should we select when reducing dimensionality of data?

Better than a scree, even in beautiful settings. Very often we find ourselves handling large matrices and, for multiple different reasons, may want or need to reduce the dimensionality of the data by retaining the most relevant principal components. A question that arises then is how many such principal components should be retained? That is, what are the principal components that provide…

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Simplifying Freedman-Lane

Simplifying Freedman-Lane, the permutation method used in randomise and PALM.

Doing a permutation test with the general linear model (GLM) in the presence of nuisance variables can be challenging. Let the model be:

where is a matrix of observed variables, is a matrix of predictors of interest, is a matrix of covariates (of no interest), and is a matrix of the same size as with the residuals.

Because the interest is in testing the relationship between and ,…

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The German tank problem and the novel coronavirus.

The German tank problem and the novel coronavirus.

We often think, perhaps narrowly, that statistics are a way to summarize large amounts of data. For example, we can collect data from thousands of subjects, and extract a single number that tells something about these subjects. The famous German tank problem shows that, in a certain way, statistics can also be used for the opposite: using incomplete data and a few reasonable assumptions (or real…

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Redundancy in canonical correlation analysis

Redundancy in canonical correlation analysis

In canonical correlation analysis (CCA), the absolute value of a correlation is not always that helpful. For example, large canonical correlations may arise simply due to a large number of variables being investigated using a relatively small sample size; high correlations may arise simply because there are too many opportunities for finding mixtures in both sides that are highly correlated one…

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A fresh Octave for PALM

A fresh Octave for PALM

PALM — Pemutation Analysis of Linear Models — uses either MATLAB or Octave behind the scenes. It can be executed from within either of these environments, or from the shell, in which case either of these is invoked, depending on how PALM was configured.

For users who do not want or cannot spend thousands of dollars in MATLAB licenses, Octave comes for free, and offers quite much the same…

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Installing NiDB

NiDB is a light, powerful, and simple do use neuroimaging database. One of its main strengths is that it was developed using a stack of stable and proven technologies: Linux, Apache, MySQL/MariaDB, PHP, and Perl. None of these technologies are new, and the fact that they have been around for so many years means that there is a lot of documentation and literature available, as well as a myriad of…

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How do we measure thickness, area, and volume of the cerebral cortex?

There are various ways one could estimate morphometric parameters of the cortex, such as its thickness, area, and volume. For example, it is possible to use voxelwise partial volume effects using volume-based representations of the brain, such as in voxel-based morphometry (VBM), in which estimates per voxel become available. Volume-based representations also allow for estimates of thickness, as…

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