Readme.md

Manipulating text, notes and other data in Matlab

Session aims

The aims of this lesson are:

• use curl to download some data from a website (no browser, terminal)
• (check out the matlab equivalent(s): webread() and websave() )
• inspect file in bash/terminal and then load into matlab

Mystery / puzzle

Given a nifti data set (4d FMRI data), and a mystery timecourse (1d), find the spatial location of the signal [x,y,z] coordinates

Info

Overall aim: Given a timeseries (1D vector) from a larger (4D) dataset, find the [x,y,z] coordinates from which the 1D signal was taken.

• 1D data is available at this address: https://raw.githubusercontent.com/schluppeck/dafni/master/matlab_text/mystery-timecourse.txt

• 4D data from which the signal was taken is dafni_01_FSL_4_1.nii

Sub-aims:

• in groups of 3-5 (10min), make a list of things you need to achieve to solve this problem.

  • data?
  • meta-data?
  • what idea / approach might give you the answer?
  • what matlab constructs will help you?
  • there are more than one way to do this... can you see alternatives?
  • what's tells you that you have found the correct location?

• now that we have a plan, let's outline the steps we'll take as comments in a matlab script.

• ... and then let's do it.

• to see how to load content / data directly from a web address / remote, without saving an intermediate file, look at this page.

• (bonus) can you see how to adapt the code for sliceview() so it can accept 3D and 4D data stored in a variable in matlab (rather than loading from a file). You could use this to visualise various results from your mystery / puzzle solving?!

Reflection

In the last few minutes of today's class - let's think about a few things that you have met in this lab class.

• What do you think was really useful?
• What was hard?
• What will you want to follow up and develop further?