Hello Freesurfer community,

I am trying to configure first level FIR analyses and contrasts for an event related task based on the design in the attached paper. I have 3 conditions (self, other, case) plus fixation. I believe the time window is 30 sec with 11 frames, 12 time points and the TR = 2.5 sec:

Timecourse:        -5   -2.5   0    2.5  5   7.5  10  12.5  15  17.5  20  25 

Timepoint:          0     1       2    3     4    5     6    7        8     9      10  11

The paradigm file for 1 of my 3 runs (attached) was developed using Optseq with Doug’s help, and I believe the TER in this case would be 2.5 sec. Do the following commands look correct?

mkanalysis-sess -analysis selfotherfir.lh -TR 2.5 -refeventdur 2.5 -paradigm self.other.par -event-related -fsd bold -surface fsaverage lh -nconditions 3 -timewindow 30 -fir 5 30 -TER 2.5 -per-run

mkcontrast-sess -analysis selfotherfir.lh -contrast self-v-other -a 1 -c 3 -no-sumdelays -rmprestim

I want to be able to view timecourses at each time point (hence the -no-sumdelays flag) in tksurfer (or freeview) but I am not sure about using the -rmprestim flag. Is there any instance when I would not want to remove baseline shifts?

Thanks for your help!

Angela

Angela Fang, Ph.D.
Assistant Professor of Psychology, Harvard Medical School
Department of Psychiatry, Massachusetts General Hospital
OCD and Related Disorders Program
185 Cambridge Street, Suite 2000

Boston, MA 02114

Email: afang@mgh.harvard.edu
Phone: (617) 643-7717
Fax: (617) 643-3080