Hi Maya, you could create 3 separatestacks with isxconcat-sess (A, B, A-B), then create the mask you want with mri_binarize, something like

mri_binarize --i A.nii --min 0.00001 --mask B.nii --mask-thresh 0.00001 --o A-and-B.nii

Then use this as the --mask input to mri_glmfit.

You should also check with a statistician that it is ok to do this type of masking. I vaguely remember removing the capability because it was a biased analysis.

doug

On 09/10/2013 03:37 PM, Maya Rosen wrote:

Hi All,

I have two conditions of interest in my GLM analysis, Condition A and Condition B. I would like to make a contrast of Condition A and Condition B that includes only those vertices that are significantly positively activated when compared to the Passive Viewing baseline. In other words, I would like to mask anything that is Passive > Condition A or Passive > Condition B and only include Condition A > Passive and Condition B > Passive when contrasting Condition A and Condition B, so as to limit my contrast to changes in /activation /in the two conditions, not /deactivation/.

I see that in an older version, when isxavg-re-sess was used, there was a flag --trunc that would allow you to set the negative values to 0. If there is a way to do this in the v 5.1.0, I could then perform a second level contrast of positively activated Condition A and Positively activated condition B.

Is there a way to exclude the negatively activated voxels from the Condition A vs Passive and Condition B vs Passive contrasts when looking at Condition A vs Condition B? I would like to do this statistically, not just at the map level.

Thank you for your help!

Maya

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