Running 3dLME using region of interest mask

AFNI Message Board
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Dear AFNI users,

I am attempting to run a 3dLME on just the hippocampus area. I keep the original LME script as it is except that I changed my whole-brain mask to this specific hippocampus mask I created (I have also made sure the mask has the same resolution as my input images). However, once I executed the script, it just stuck after reading all the input files… Since there are no specific errors given, I am not sure what to do at the moment. I am guessing AFNI 3d LME will allow to run not only on whole-brain mask but also regional mask, but is this assumption wrong? Or I have mistaken on any specific set up steps in order to have this particular type of analysis run?

Many thanks in advance.
Sarah

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Sarah,

3dLME should work fine with any size of mask. Make sure you have the most recent version of AFNI before your run your new 3dLME script. Alternatively, you could just apply the mask using 3dcalc to the 3dLME output from your original script (with the whole-brain mask).

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Thanks very much!!!