There are two issues here:
1. Make sure that all of your subjects have been reconstructed with the same version of freesurfer (it looks like you have done this).
2. If you've used an "older" version of freesurfer for the recon, then render (ie, paint) your results on average7 (the default). If you've used a "newer" version (which you have), then render them on fsaverage.
doug
On Wed, 7 Jun 2006 raij@nmr.mgh.harvard.edu wrote:
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