You don't have to specify a threshold at all. In that case it will average over the entire structural ROI. What you have below will average only over the positive values. What about the current stream is not streamlined? Or, how could it be improved?

doug

Adam Nitenson wrote:

Hello Freesurfers,

 I am currently running ROI analyses (dACC) and want to plot the

timecourse of hemodynamic responses to a cognitive task (2 conditions) in a group of subjects. I have been using func2roi commands such as

func2roi-sess -roidef lh_dACC -analysis RM_correct_error -anatlabel lh.dACC -maskcontrast error_vs_correct -maskthresh 0.000000001 -masktail pos -maskframe 5 -maskmap sig -sf /autofs/space/ventzl_036/users/RespMon12C/subject_lists/caitlin_SZerrorcorrect.txt -d /autofs/space/ventzl_036/users/RespMon12C/subjects

and then roisummary to generate charts from which I create a hemodynamic curve through data manipulation.

I was recently informed that there should be a way through which I

could automatically plot such a hemodynamic curve, and that this method might not require a designated threshold as func2roi does (as we want any activation in the ROI to be considered). Is there any way to create a more automatic, streamlined hemodynamic response curve, or are func2roi and roisummary the standard means of doing this?

Thanks,

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer