Batch processing in SPM
Statistical Parametric Mapping (SPM) is a complete suite of Matlab functions that can be used for the analysis of brain imaging data from image preprocessing to statistical analysis. The software is made freely available...
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Extracting volumes from a 4D nifti file
With the introduction of the Nifti format, a series of functional MRI volumes can now be stored as a single 4D (3D space + 1D time) nifti file. This is very handy especially when...
Splitting 4D Nifti file into a series of 3D files in Matlab
NIfTI-1 is a data format proposed by the NifTI (Neuroimaging Informatics Technology Initiative) DFWG (Data Format Working Group) that can be used for storing neuroimaging datasets (e.g. MRI, functional MRI, etc.). This format is adapted from the...
Using SSH for passwordless remote login
Secure Shell or SSH is a network protocol allowing secure data exchanges between two networked devices. It is designed to replace Telnet, which sends information over the network in plain text making it susceptible...
Data types and data structures in R
In this post, I will outline the basic mathematical operation in R, the different data types you can define, and how to manipulate these data types. If you have not yet installed R, you...
Getting started with R
This is a multi-post tutorial on how to get started with the programming environment called R. R is very useful for researchers doing data analysis as part of their work. It is a free...
Tools for brain imaging data analysis
Here’s a list of the tools I mainly use for the analysis of brain imaging data including anatomical T1-weighted magnetic resonance imaging (MRI) data, functional MRI (fMRI), and diffusion MRI (dMRI), among others: SPM12...