Hi, Backround: I am running a fixed effects group analysis with fsaverage (mne305) as the target brain, and merging the activations across subjects on the spherical surface. The individual functional sessions have been co-registered to the individuals' structural brain reconstruction (i.e. the register.dat file inside the bold directory links the functional and structural data within subjects only).
Problem: I am not sure how to set the group analysis func2sph-sess and paint-sess "target brain" parameters correctly. Version and environment: I am using the current Martinos Center FreeSurfer standard installation (vs. >3) under nmr-std-env and all the structural reconstructions are new as well. Outline of the analysis (list of commands): preprocessing mkanalysis-sess.new selxavg-sess mkcontrast-sess stxgrinder-sess func2sph-sess <- sphsmooth-sess isxavg-fe-sess stxgrinder-sess paint-sess <- Specific question (with possible answers): *** 1 *** Should I set the target brain already at func2sph-sess: func2sph-sess -analysis XXX -sf sessid -df sesspar -trgsubject fsaverage (if the -trgsubject setting is omitted, then the target appears be the default = ico order 7) *** 2 *** Or is it sufficient (if I ignore the -trgsubject parameter above) to set: paint-sess -analysis XXX -contrast YYY -subject fsaverage -space sph -isxavg fixed -s fegroup -df group.sesspar (here fegroup = the folder where the fixed effects analysis is stored, set at isxavg-fe-sess -s fegroup) *** 3 *** Or must/should I do both 1 and 2 of the above. I am using surf-sess/tksurfer to view the results and set -subject fsaverage even there. I get results that look reasonable either way. I just wonder what is the difference between the methods, and if either method is unambiguously correct. Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
