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firstAnalysis.md

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First analysis (FSL, UNIX, ...)

The aim of this session is to analyze the data we acquired with 3T functional MRI in our simple cognitive neuroscience experiment.

In outline, the first steps will be very similar to what you may remember from another course (C84FIM), where we had a demonstration & walk-through of a simple data sets.

Can we make to this, today?

Have a look at the PDF to refresh your memory.

The plan for here is:

  1. copy data across to a directory in your space
  2. organise data in folders
  3. start up Feat_gui &
  4. provide all the necessary info in the GUI interface
  5. hit Go! and watch for progress in web browser
  6. dig around in the resulting folders and files

Organise the data into folders

Do this "by hand" - using mouse clicks in the macOS operative system for now. We'll see how to use command line calls in the Terminal soon. Think about which files are:

Take 2 minutes with your neighbours to discuss the following

  • How can you tell (in words?)
  • What tools / commands could you choose to check / inspect?
  • What are good ways to keep track of some key information? In the same place? Somewhere else? What are the advantages / disadvantages of those options?

Create a directory in your home

# first an "umbrella" folder, then one for subject 2
mkdir ~/data/
mkdir ~/data/subject-A/

# navigate into data directory
cd ~/data/subject-A/

# COPY the files from
# /Volumes/practicals/ds1/2020-dafni/subject-A
# TO here (.)
#
# HOW?

Some initial steps / warm-up

  1. Orient the MPRAGE image into the "standard" orientation that most tools will expect. This is not always necessary, but if there are issues with "alignment" in your fMRI analysis, this step can help:
# navigate into data directory
cd ~/data/subject-A/

# identify the MPRAGE image.
# mine is: ` ???  `

fslreorient2std *sMPRAGE*.nii  mprage

# if you want to skipt this step, you could also just move / rename
immv *sMPRAGE*.nii mprage
  1. skull strip that anatomy
# inspect, if ok, then skull strip and also make a  mask (-m)
bet mprage mprage_brain -m
  1. look at the images using fsleyes

Set up the analysis using the GUI

Start up feat either via the fsl menu or directly.

# navigate into data directory
cd ~/data/subject-A/

# then pick FEAT FMRI analysis
fsl &
# - OR -
Feat_gui &

Key information

  • What is the name of the 4D data set?
  • Check total volumes and TR are picked up correctly.
  • Consider all the options in the Pre-stats tab.
  • Registration. We to register to a Main structural image as well as into Standard space.
  • if you use the BBR method you need to use the _brain.nii image we made in a previous step. This method is pretty cool, but if not given the right files it tends to run for a long time [viz infinite].
  • Stats. We want to specify a full model. To do this, we need to use the face/object/scene.txt files here

Eye candy

Register onto a nicer image:

# the renderhighres tool!
# get minimal help:
renderhighres

# actually run it:
renderhighres *.feat highres highres 1

You can then look inside the hr directory and look at the files called rendered_thresh_zstat.