This is with FSFAST? You can run isxconcat-sess on both analyses. For version4.X, this will create output files like lh.ces.mgh. If you keep the subject order the same for both analyses, then you can use mris_calc to take the difference between them (ie, a paired analysis). You will then have a file with number of frames equal to the number of subjects, each representing the difference between the two experiments. You can then run a one-sample-group-mean (--osgm) with mri_glmfit.

You should make sure that all the imaging parameters are the same between the two experiments.

doug

Shahin Nasr wrote:

Hi Doug and freesurfers,

 My subjects have participated in two independent experiments 

within two different sessions (e.g. experiment 1 in day 1 and experiment 2 in day 2). Now I want to see if the contrast between conditions of experiment 1 and 2 is significant or not. For instance I want to compare condition_1 of experiment_1 with condition_2 of experiment_2. How should I do that? Actually I want to see the contrast map and then apply ROI-based (fun2roi) analysis.

Thanks for your help Shahin Nasr

PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School