FMRI Analysis: Within and between group analyses

Within-group Analyses

3dTTest Script

SUMMARY: Calculates t-tests on specific model coefficients – that is to say, on your contrasts of interest. 3dttest can be used for within and between group comparisons. You’ll need two separate 3dttest scripts for this purpose.
INPUT: the z*reg+orig.* output from the reg script
You’ll also need to pull coefficient tags from the z*reg+orig file. Find the correct coefficient tag by using the 3dinfo command on the z*reg+orig output file. OUTPUT: .BRIK & .HEAD files – one pair for each contrast of interest.
RUN FROM: the scripts folder
RUN ON: everyone within your group at the same time
NOTE: Before you run the script you’ll need to create a folder called “ttests” in the experiment root directory (that is, in the expt’s broadest directory level where subject folders are located).

The 3dttest script used for within group analyses is sufficiently similar to that used for between-group analyses that we will only cover a few lines of code in this section. (To learn more about the 3dttest script, see discussion in the between-group analyses section that follows.)

Between–group Analyses

3dTtest Script

SUMMARY: Calculates t-tests on specific coefficient maps – that is to say, on your contrasts of interest. 3dttest can be used for within and between group comparisons. You’ll need two separate 3dttest scripts for this purpose.
INPUT: the z*reg+orig.* output from the reg script
OUTPUT: .BRIK & .HEAD files – one pair for each contrast of interest.
RUN FROM: the scripts directory
RUN ON: everyone from both groups
NOTE: Before you run the script you’ll need to create a folder called “ttests” in the experiment root directory (that is, in the expt’s broadest directory level where subject folders are located).

The 3dTtest script can be found in the “scripts” folder in most experiment home directories. It calculates t-tests on fit coefficients of specific regressors – that is to say, on your contrasts of interest, represented now by the output of your reg script (the z*reg+orig.* file). The 3dttest script pulls the coefficients from the reg output and compares with zero (within-group) or the other group’s data (between-group). For example, it can effectively look at whether there was greater activation at anticipation for high win (usually tagged with 1 in the lookup tables) trials versus low win trials (usually tagged with -1 in the lookup tables).

The 3dttest script outputs .BRIK & .HEAD files – one pair for each contrast. These are what you view in AFNI. They’ll be in your ttests folder a format that looks something like:

$ pvnant10c9s+tlrc.BRIK
$ pvnant10c9s+tlrc.HEAD

That is

$ contrastname_#subjs+tlrc.*

You will have a different 3dttest script for each group (within group statistics), and usually only one for between-group analyses. These scripts will call up all related model coefficients (within group or between group). On occasion for less stable models you’ll have different 3dttest scripts for different between-group contrasts (eg, for endowment and risk).

The script begins by warping each subject’s z*reg+orig file into Talairach space with adwarp. It does this by taking the set of rules you created when you warped your anatomical data, and applying the exact same warp to all of your functional data. The adwarp function can also resample voxels into a new resolution [ the –dxyz 2.0 flag, for example, resamples the input into 2mm cubed voxels]. You can edit the resample size in the 3dttest script by finding that flag and editing the number that follows.

Discussion of resampling – ask Brian.

3dttest then moves on to ttests on regressors using the command 3dttest.

Here, the 3dttest script is assessing how much of an effect each regressor has on the brain activation of interest. The t-score is derived by dividing the beta value of each regressor by its standard error term. We can then assess if these t-scores are significant or not. In other words, we can now know whether our regressors are significant predictors of the brain activation.

After completing the ttests, the 3dttest script applies the 3dmerge command to convert your t-stats to z-scores, thus creating a more intuitive stat to view in AFNI.

Before you run the 3dttest script, go to the parent experiment folder and create a ttests subfolder. The script will look for this folder and put its output files there. AFNI, in turn, looks for the folder when you select the overlay. If your files are present, you’ll be able to select your contrasts of interest!

span@dmthal riskfmri]$ mkdir ttests

Now edit your 3dTtest script appropriately.

span@dmthal riskfmri]$ cd scripts
span@dmthal riskfmri]$ emacs 3dttest

You’ll be able to pull the appropriate sub-brick # of the listing for the coefficient of your contrasts from zriskbasicreg+orig or whatever your reg script output file in the format z*reg+orig is named. You can do this by using the 3dinfo command on the file (in this case a zfile output from the risk task):

span@dmthal riskfmri]$ 3dinfo zriskbasicreg+orig.*

Here is a commented within-group 3dttest script to peruse. To see an example of a between-groups 3dttest script, go to dmthal:/data3/bipomid/scripts/3dttestantoutreg#b.

Here the bracketed number [10] after each subject is the coefficient tag we’ve pulled for that particular contrast from the z*reg+orig output of the reg script. Each contrast will have only one coefficient tag.

The –prefix flag syntax basically means that whatever entry (argument) follows it is the name of the output of that contrast’s t-test. In this case, our contrast is reward versus neutral anticipation, so our output name is trvnant3 (t for t-test, 3 for number of subjects).

-base1 is what you’re comparing all the coefficients to (here 0) -set2 is your data -session flags where you want to put your output

Here we’ve commented out (#) some contrasts we’re probably not going to use in this experiment (ant and out).

Note: be sure to edit the coefficients appropriately for each new experiment. Note that 3dttest is also run FROM the scripts directory (in the program there are lines that instruct the script to look for the subject directories).

span@dmthal scripts]$ ./3dttest

Remember to run your 3dttest scripts each time you add a new subject or a number of subjects to the group. You’ll need to ratchet up the number in the contrast file names, as well as add the subject to the list of subjects whose directories are searched by the scripts. It’s worth keeping those old files around, though: you may want to see how your data changes as you add more subjects. Keep in mind that you won’t need to re-run your reg script on everybody; only on the subject who’s been added.

ANOVA

An ANOVA tests for significant differences between means from two or more groups.