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
[EMAIL PROTECTED] wrote:
Thanks Doug, just a quick check that I understood correctly:
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).
Correct
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.
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 [EMAIL PROTECTED] 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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