Overview¶
The material here is for students doing the CLNE0068: Research Methods and Data Analysis in Human Neuroscience course at UCL.
For the first-level analysis, each student should download and analyse a different subject’s data from the ‘MRI data’ link in the ‘Data analysis resources’ section. Download the attached Excel file and find out which subject you will be working on from your Candidate Number. At a later stage, we’ll be combining everyone’s results for group analysis, so it is important you work on your assigned subject.
Data¶
The entire original dataset is from 19 participants (8F & 11M, ages 23-37 years) and described in the paper by Wakeman et al (2015). This tutorial only uses a subset of the original data. Originally, there were nine runs of fMRI for each participant, but we will use only the first two.
For subject XX, the data you should have are:
sub-XX/anat/sub-XX-T1w.nii. A T1-weighted MPRAGE MRI scan (TR 2,250 ms, TE 2.98 ms, TI 900 ms, 190 Hz/pixel; flip angle 9°) of 1 mm isotropic resolution.sub-XX/func/sub-XX_ses-mri_task-facerecognition_run-01_bold.nii. The first run of functional data, acquired using an EPI sequence (TR 2000 ms, TE 30 ms, flip angle 78°), with 208 volumes. Slices were acquired interleaved, with odd then even numbered slices (where slice 1 was the most inferior slice).sub-XX/func/sub-XX_ses-mri_task-facerecognition_run-01_events.nii. A MATLAB file containing the onset times of the three types of stimuli for the first fMRI run. The file contains three variables:famous,unfamiliarandscrambled.sub-XX/func/sub-XX_ses-mri_task-facerecognition_run-02_bold.nii. The second run of functional data, acquired using an EPI sequence, with 208 volumes.sub-XX/func/sub-XX_ses-mri_task-facerecognition_run-02_events.nii. A MATLAB file containing the onset times of the three types of stimuli for the second fMRI run.
Experimental design¶
For the sake of this analysis, three types of stimuli (trial-types) were used
- Famous Faces. Grey-scale photographs of people the participants are likely to recognise.
- Unfamiliar Faces. Grey-scale photographs of random people, but with similar properties to the famous faces.
- Scrambled Faces. Essentially just slightly smooth random noise, but with some properties similar to that of the face data.
Participants saw the pictures projected onto a screen in front of them (subtending horizontal and vertical angles of 3.66° and 5.38°), against a black background and with a white fixation cross in the center. Between stimuli, participants saw a central white circle. The fixation cross appeared between 0.4 and 0.6 seconds before each picture, and these were shown for between 0.8 and 1 seconds.
Participants were told to fixate on the circle or cross throughout the fMRI runs, and not to blink while the cross-hairs or pictures were visible. To sustain participants’ attention, they were asked to press a key with either their left or right index finger, depending on whether they regarded each image as more or less bilaterally symmetric than average. .
Analysis¶
Start up MATLAB and type spm fmri at the
MATLAB prompt. SPM will then open in fMRI mode with three windows (1)
the top-left or “Menu” window, (2) the bottom-left or “Interactive”
window and (3) the right-hand or “Graphics” window.
