event-related fMRI

This page describes how to analyze fMRI data from a single individual using FSL. FSL is a powerful and free tool to measure task-related changes in the brain’s blood flow. This tutorial also shows how to conduct region of interest analysis using MRIcro’s peristimulus plotting package. To complete this tutorial you will need:

To conduct FSL single subject data processing you will need
1. FSL installed on your computer (you should get VMware player if you are using a Windows computer).
2. The workshop DVD includes a sample dataset, when you launch VMware player the file will be located in the ‘data’ folder (/home/user/data), you can also get this online by downloading efmridata.zip. This includes a 200 volume fMRI session (n20060219_201158s006.img), text files (onsetL_1dummy.txt,onsetR_1dummy.txt,onsetU_1dummy.txt) that describs the events that occurred during the fMRI session.

About the sample dataset

This was a simple finger tapping task. The screen rapidly flashed (every 1050ms) with an arrow (<,> or ^). When the arrow pointed up (^) the participant was asked to rest, when it pointed right (>) they were intstructed to tap their right index finger, and when it pointed left (<) they were requested to push their left index finger. These events repeated for the whole scanning session (200 volumes, about 10 minutes). The order of stimuli was a ‘permuted block design’ – subsequent trials tended to show the same visual stimuli, but there were 100 exceptions to the pure block design. The first fMRI scans will be discarded (as these appear brighter as the T1 effects are not saturated). The onsets of the tasks are recorded in the text files (onsetL_1dummy.txt,onsetR_1dummy.txt,onsetU_1dummy.txt). The image below shows the three event types (left, right or up arrow) as marks at the top of the image (with blue, red and green indicating the stimuli types). The colored lines show the expected HRF response.
task order

FSL single subject data processing

Start FSL by clicking on the fsl shortcut within the computer desktop, or by starting typing ‘fsl’ from the command prompt. Note that if you type ‘fsl &’, the command console under which FSL is running will not be “frozen” by FSL, but can be used for other commands.
By typing fsl, a user interface (the one with a fossil fish on its top) appears. This interface contains several options, but the one to be used now for fmri is ‘FEAT FMRI Analysis’ button. Press the corresponding button and this will open the Feat interface.(The forthcoming steps are described for use in FEAT version 5.43)
The feat interface has two top buttons. The following analysis is a first level analysis (within one single subject), and it is a full analysis (involving preprocessing of the data, the statistical spinnings of fmri analsysi and post-stats registrations).
The FEAT interface five tabs across the top portion of the screen, oriented in a horizontal line. The fmri analysis can be set by defining the parameters within each one of those buttons, in a left to right order:
- within Misc Tab: – leave ‘Featwatcher’ checked to gauge the progress of the fmri analysis. – set the delay to start the analysis to a number different to zero: we want to compute this analysis immediately.
- within Data Tab: – Number of analysis is set to one. – Press select 4D data. Browse to the folder in which the 4D data file is stored and select the .hdr of the corresponding file (e.g. /home/user/data/n20060219_201158s006) After selecting the 4D file, the number of volumes will automatically be displayed. In our case 200. – enter the TR. In our case 3.0. – set the delete volumes to 1 – set the high pass filter cutoff to 100 s. You can set the output directory: you must be able to write to this directory (the output directory can not be your DVD drive). If you leave it blank, it will write the results in the same folder where the 4D data is. FEAT write the results in a folder called “4Ddataname.feat”. In our case fds.feat. If you re-run the analysis, it will create a second folder called fds+.feat, and so on.
- within Pre-stats: – Slice timing correction could be set to regular up (0,1,2…n-1) . – Motion correction is done with Motion Correction using FMRIB’s Linear Image Registration Tool – MCFLIRT. – Keep Brain Extraction checked. – Spatial smoothing FWHM set to 8mm (between x2-x3 the raw resolution of the functional imaging). – Lets keep Intensity Normalization (equivalent to Grand Mean Scaling) unchecked. – Temporal filtering Highpass checked.
- Within Stats Tab – Simple model setup could be used for alternating designs like ABAB, or ABCABC. Our design is a bit more intricate so press the ‘Full Model Setup’ button (this can also be used for event related designs). – Clicking full model setup opens a General Linear model interface. Within this interface, follow the steps: – The number of original EV (original EVS – explanatory variables, or simply put: conditions) is set to 3, because we are interested in the response to the ”left”, “right”, “up” conditions. – Each EV is setup separately. – The basic shape of the wave form that describes the stimulus that we wish to model is defined by a custom file expliciting the time in seconds of the onset of the stimulus, how much time (also in seconds) the stimulus last, and the value of the input. This requires a .txt file containing a matrix under which the columns are the variables stated above (i.e., first one time of onset, second one the duration, and the thrid one the value) and the rows represent the stimuli.
- Setting Up Conditions: This is set as follows: initialls set the number of original EVs to the number of condictions (two). For each condition, do the following: first choose the ‘Custom (3 column format)’ from the ‘Basic Shape’ pull-down menu, second browse to find the file left_onsets2dum.txt (for the first condition) and left_onsets2dum.txt (for the second condition), third set the convolution (which is the form of the Hemodynamic response function that will be applied to the basic waveform) to ‘Gamma’, fourth maintain Phase, Stddev and Mean Lag as defaults (respectively 0,3 and 6 secs), fifth apply temporal filtering. As we are using a event related design, I suggest making sure temporal derivative is checked.
- Setting Up contrasts: Once these parameters have been entered click on ‘Contrasts & F-tests’ tab. In theory, we could create quite a few statistical comparisons, for example, here are five possible contrasts of interest:
- Alternatively, we could only look at our two favorite conditions (left > right and right > left, as shown below).
- Press Done to continue.
Within Post_stats Tab- Do not use a pre-threshold masking – Maintain defaults for thresholding (Cluster analysis, Z threshold of 2,3, cluster P of 0.05) – Maintain defaults for rendering and contrast masking.
Within Registration Tab: We do not have a structural image for this particpant, so do not check the ‘Main structural image’ checkbox.
Make sure the normalization to standard space uses 12 DOF (12 parameters: rotation, zoom, shear, translation in 3 dimensions) – this is not the default, but works much better. *See Footnote
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Press the ‘Go’ button on the bottom left. and Featwatcher will be opened and will show you the progress of the analysis. After the analysis finishes, Feat watcher will bring you a message stating the time it finished and where the folder with the results is.
Look for the folder called fds.feat that will probably be in the same folder where the 4D data is.
To assess the analysis click on report.html and the internet browser used as the default in your computer will bring the page containing information on the results.

WebOutput

event-related fMRI

About the sample dataset

FSL single subject data processing

Make sure the normalization to standard space uses 12 DOF (12 parameters: rotation, zoom, shear, translation in 3 dimensions) – this is not the default, but works much better. *See Footnote