Basically, you're right (it subtracts the average of each condition), but the answer is considerably more complicated! It will create a box car of 18 sec for Condition 1 and convolve that with a gamma function to create the regressor for Cond 1. It will create a boxcar of 3 sec for condition 2, etc. It then fits the observed waveform to get estimates of the amplitude to each each condition, then does the subtraction. I don't know why you're seeing negative activation in occipital cortex. On thing you might try is to change the condition IDs so that your blank screen is condition 0 instead of 1 (need to renumber the others as well), though I doubt this will make a difference.

doug

Zeidan, Mohamed A. wrote:

I was wondering if someone could help me answer a relatively simple question:

I set up a paradigm file (called recall.par) as follows:

0 1 18 2 21 3 27 1 45 2 48 3 and so on... Where in the right column, condition 1 is blank screen, 2 is a room with a lamp, and 3 is the lamp turned on.

My question is:

When I run the analysis to compare condition 2 to condition 1, does it subtract the average activation from 18-21 seconds minus the average activation from 0-18 seconds? Or does it simply subtract timepoint 18 from timepoint 0? Or what?

When I set up a contrast to do condition 2 minus 1, I expected visual cortex activation, but instead, I saw deactivation. I am trying to figure out why this is the case. Any help would be greatly appreciated.

thanks, Moe

Mohamed Zeidan Research Assistant Behavioral Neuroscience Laboratory Department of Psychiatry Massachusetts General Hospital (617) 643-4756

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Lena Palaniyappan *Sent:* Monday, March 22, 2010 4:43 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Displaying parcellation labels asegstats2table

I am trying to obtain mean intensities of Destrieux parcellations using the following command.

asegstats2table --subjects <subjid vbms08> --meas mean --statsfile lh.aparc.a2009s.stats --tablefile somename.txt

But the output text files does not contain any label names. instead it contains the following as output

Measure:mean 2.184 2.442 2.307 2.755 2.869 2.632 2.360 2.073 2.901 2.617 2.186 2.890 3.070 2.748 2.759 2.777 3.201 3.737 2.801 2.376 2.893 1.964 2.967 2.928 2.886 2.778 2.426 2.316 2.805 2.567 2.320 2.522 2.809 3.307 4.177 2.774 2.732 3.128 2.232 2.691 2.258 0.737 2.148 3.682 2.066 1.856 1.972 2.999 2.651 2.521 2.978 1.969 2.207 2.443 2.369 2.455 2.099 1.856 1.821 2.293 2.698 2.386 1.973 2.096 2.393 2.129 2.122 1.981 2.359 2.276 2.645 2.204 2.382 2.379 2.709 vbms08 0.509 0.525 0.482 0.442 0.444 0.706 0.706 0.595 0.551 0.615 0.468 0.499 0.338 0.518 0.472 0.588 0.54 0.881 0.606 0.554 0.453 0.518 0.949 0.763 0.565 0.53 0.52 0.492 0.491 0.522 0.731 0.909 0.393 0.518 0.631 0.448 0.953 0.673 0.305 0.631 0.521 1.353 0.552 0.828 0.595 0.457 0.607 0.538 0.643 0.5 0.721 0.43 0.471 0.53 0.492 0.333 0.471 0.457 0.451 0.489 0.549 0.452 0.427 0.661 0.608 0.531 1.182 0.41 0.476 0.481 0.777 0.559 0.677 0.547 0.417

How can I get the parcellation labels displayed?

Cheers Lena

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*Lena Palaniyappan *Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH

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