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interpreting behavioural pls outputs
jesseH
Posted on 07/28/08 10:03:42
Number of posts: 8
jesseH posts:

I'm having some trouble interpreting the results output from behavioural pls. 1. Understanding the coloured weights (saliences) across the brain (and how they relate to the scatter plots in the brain score overview window): (a) do BOTH blue and yellow areas represent voxels whose intensities correlate with behaviour, with only the polarity changing (yellow = same polarity as the shown correlations; blue = reversed polarity from the shown correlations) OR (b) do the colours represent a breakdown of the correlations: in this case, I have a negative correlation, so: blue weights representing areas that are associated with large behavioural scores and yellow areas representing areas of low behavioural scores. 2. I guess, more generally, I'm confused about how to interpret the scatter plots in the brain scores overview. What does it mean that *brain scores* are negatively correlated with behaviour? Does that actually tell me anything about how voxel intensities are correlated with behaviour??

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jesseH
Posted on 07/28/08 10:21:05
Number of posts: 8
jesseH replies:

Apologies for not reading these archives as carefully as I should have done before posting!  I can see from a historical post, that the answer to my first question is (a):  The saliences tell me where voxels show the same (or opposite) correlation depending on the colour of the salience.

But I would still appreciate some insight as to how to interpret the correlations themselves.  Is it correct to assume that for salient voxels, there is a correlation between BOLD activation and the behavioural measure?  Or do these correlations represent something more obscure: the overall correlations are between brain scores and behaviour, but I'm hazy about exactly what brain scores are and whether they allow me to draw any conclusions back to the actual brain activity


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rmcintosh
Posted on 07/28/08 10:31:19
Number of posts: 394
rmcintosh replies:

Hi Jesse,

Glad you were able to get a partial answer in the archive. As for your current question:

But I would still appreciate some insight as to how to interpret the correlations themselves.  Is it correct to assume that for salient voxels, there is a correlation between BOLD activation and the behavioural measure?  Or do these correlations represent something more obscure: the overall correlations are between brain scores and behaviour, but I'm hazy about exactly what brain scores are and whether they allow me to draw any conclusions back to the actual brain activity


The salience/weight for a voxel is proportional to its correlation, or to the difference in the correlation if your behavior profile (weight or LV) indicates a task or group difference. The brain scores are a summary across the entire image and depend, for a given subject, on the balance of activity between positively and negatively weight voxels: more positive brain score, more activity in positively weighted voxels. The correlation between these scores and the behavior you will note is the same pattern as in the behavior LV. In fact, the behavior LV you see in the PLSGUI is essentially a normalized version of the correlations (unit normal vector). The pattern is the multivariate expression of the brain-behavior correlation so it is vital to your interpretation: i.e., is the correlation pattern significant (permutation test) and reliable (bootstrap confidence intervals on the behavior correlation). The voxel weights, and bootstrap ratio, add to this by idenifying the voxels with the more reliable contribution to the pattern.

Does this help?

Randy


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jesseH
Posted on 07/28/08 10:53:09
Number of posts: 8
jesseH replies:

I think so. In my case, I'm looking at correlations between accuracy on a 1-back task and brain activity in 3 stimulus conditions (untrained faces, untrained houses, and trained houses). The scatter plots show negative correlations for the two house sets, and zero correlation for the face set. You state: "or to the difference in the correlation if your behavior profile (weight or LV) indicates a task or group difference" So, in my case, I assume that because the face condition doesn't seem to contribute to the LV at all (no correlation, and a weight of near-zero in the behaviour LV plot), and both other conditions are negatively weighted, then yellow would indicate negative correlations and blue positive correlations between brain activity and behaviour. Correct? A second question: As I was scanning these archives, I discovered that my earlier task pls was conducted incorrectly, but I'm at a loss of how to fix it: The task pls that I ran compared these three conditions in session 1 (prior to training the trained house set) versus session 2 (after training). I ran this by treating session 1 and session 2 as separate groups, but I see from your response to others that because these are the same subjects across sessions, I should have entered all 6 conditions (stimulus x session) into the same session file (treating the analysis as repeated-measures). The trouble is: I have different data files for the 2 sessions, and when defining the data files associated with each of the runs, I don't see any way of providing different data files for different conditions (as the gui is set up, the files you select for a given run apply to all conditions). I suppose I could just run the task pls as two separate analyses: one for each session, and look at whether the condition pattern changes across sessions... but what I really want to know is: do I get a significant LV that appears to be weighting session 1 vs session 2 (i.e. some overall effect of learning)?


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rmcintosh
Posted on 07/28/08 15:38:20
Number of posts: 394
rmcintosh replies:

So, in my case, I assume that because the face condition doesn't seem to contribute to the LV at all (no correlation, and a weight of near-zero in the behaviour LV plot), and both other conditions are negatively weighted, then yellow would indicate negative correlations and blue positive correlations between brain activity and behaviour. Correct?

yes - though you may have some voxels that show a weak positive correlation in the face condition

A second question:
The trouble is: I have different data files for the 2 sessions, and when defining the data files associated with each of the runs, I don't see any way of providing different data files for different conditions (as the gui is set up, the files you select for a given run apply to all conditions). I suppose I could just run the task pls as two separate analyses: one for each session, and look at whether the condition pattern changes across sessions... but what I really want to know is: do I get a significant LV that appears to be weighting session 1 vs session 2 (i.e. some overall effect of learning)?

hmm, when you say you have different data files associated with each run, does that mean different conditions were in the two runs? You could run it by using different conditions names for stuff that happened on day 2. Something like (c=condition, s=session): c1d1, c1d2, c2d1, c2d2

would that work?

Randy


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jesseH
Posted on 07/29/08 11:20:43
Number of posts: 8
jesseH replies:

Not quite. Let me try to clarify. I have two fMRI datasets for each person (session1: pre-learning and session2: post-learning). In each session, there were 6 runs that contained 3 conditions each. I want to compare those three conditions with each other, but also look for session differences (i.e. pre-learning/ post-learning differences). Before, I ran this analysis by setting up two session files for each person (pre and post). In each session file, I defined the six runs and the three conditions in each run and assigned the associated img files that made up each run. Then, I ran the analysis by assigning all the session1 (pre) files to group 1 and all the session2 (post) files to group 2. BUT, I had the same subjects across these two groups, so a repeated measures design would be more appropriate. In an earlier post, you suggested to another poster that to run a repeated measures design, all conditions should be assigned within a single session file, so that the analysis could be conducted with a single group. But, I don't think I can do that in this case. I can append 3 new conditions (for the post data) to my pre session files but, when assigning the img files to each run, I would need to assign different files to the pre and post conditions (because they come from different scanning sessions), and I don't see any way to do that in the gui.


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I'm Online
nlobaugh
Posted on 07/29/08 12:46:34
Number of posts: 229
nlobaugh replies:

quote:
Not quite. Let me try to clarify. I have two fMRI datasets for each person (session1: pre-learning and session2: post-learning). In each session, there were 6 runs that contained 3 conditions each. I want to compare those three conditions with each other, but also look for session differences (i.e. pre-learning/ post-learning differences). Before, I ran this analysis by setting up two session files for each person (pre and post). In each session file, I defined the six runs and the three conditions in each run and assigned the associated img files that made up each run. Then, I ran the analysis by assigning all the session1 (pre) files to group 1 and all the session2 (post) files to group 2. BUT, I had the same subjects across these two groups, so a repeated measures design would be more appropriate. In an earlier post, you suggested to another poster that to run a repeated measures design, all conditions should be assigned within a single session file, so that the analysis could be conducted with a single group. But, I don't think I can do that in this case. I can append 3 new conditions (for the post data) to my pre session files but, when assigning the img files to each run, I would need to assign different files to the pre and post conditions (because they come from different scanning sessions), and I don't see any way to do that in the gui.
Jesse..
you could do the following:

1) move the session2 images into the same subdirectory that holds the session1 images, ensuring that the filenaming convention for session2 images places them ^after^ the session1 data alphabetically.

2) rename your variables in your session1 session_profiles to indicate they are session1 variables

3) add in the variables for session2, and update their trial onsets to account for the session1 data (i.e, if you have 10 images  in session1, and the first trial onset for session2 was image1, the trial onset should now point to the 11th image in the directory).  Save as a new session_profile name.

this should give you a datamat for each subject that contains data for both sessions.

nancy



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jesseH
Posted on 07/29/08 12:55:45
Number of posts: 8
jesseH replies:

Ok.  That makes sense now.  I'll give that a try.  Thank you both for your help!!



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