Oh, sorry, I forgot you were doing that. Setting -trgsubject to fsaverage actually simplifies things a lot as you do not need to run the paint command (or mri_surf2surf from the last email) as everything will be on fsaverage to begin with.
doug
raij@nmr.mgh.harvard.edu wrote:
Thanks Doug, just a quick check that I understood correctly:
There are two issues here:
- Make sure that all of your subjects have been reconstructed with the same version of freesurfer (it looks like you have done this).
Correct
- 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.
Does this mean that setting "func2sph-sess -trgsubject fsaverage" makes no difference in this case (as long as fsaverage is defined in paint-sess)?
-T
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.
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