USEFUL RESOURCES
A couple of resources that I have found very useful in my work. I hope that all these links are free to share, as they are all available online.
Professor Radford Neal's code to implement Hamiltonian Monte Carlo (here). I made some modifications of this code to use in my research. That can be found in the codes at my github page. I also wrote a short review on HMC in the supplementary materials of my this paper.
The neuroconductor.org for R-implementations of MRI image processing.
John Muschelli's code to process fMRI can be found here.
For processing dMRI image, this is very useful, as well as the Brainsuite software. Brainsuite also can be run using bash code for batch processing. All the details are there in this link.
For structural MRI, this is very useful.
In neuroimaging studies, the creation of masks is also very important for targeted analysis. This can be done using FSL and a tutorial can be found here.
I often run FSL in my Windows desktop following these instructions.Â
There are R-packages available for registration, like RniftyReg.
Formulas for some basic sample size calculations in clinical research. The PASS software is very good, though paid. An alternative may be to download the trial version, which comes with all the pdf materials on sample size estimation methods for many different statistical models. For a statistician, it is a great resource to learn and use those directly.
Nice comparison of methods used for multiple comparisons can be found here.
If the data is in data.frame format, this website has codes for different types of plots using ggplot.