yesand yes doug
On 11/30/2012 10:53 AM, Alexandra Tanner wrote:
Hi Doug,
So if I run a group analysis with each contrast separately, would I then be running mri_concat to do a conjunction of the group sig maps? Also, can I merge more than 2 contrasts at once when using mri_concat? Thanks!
Alex
Hi Alex, unfortunately, you cannot compute a conjunction with the CES.
That's the problem with trying to do group-wise multi-variate analysis. Another thing you can do is to do a group analysis with each contrast separately, then do a conjunction of the group sig maps.
doug
On 11/29/2012 03:39 PM, Alexandra Tanner wrote:
Thanks for the clarification! So I will rerun mergecontrasts-sess using
the ces image on my subjects and then run mri_vol2surf and mri_concat to
get the group map. Thanks for your help! Best, Alex
Usually the contrast effects size (ces) (in SPM this is the CON image,
in FSL it is the COPE image). Univariate maps are usually passed up to the group level (the conjunction done with mergecontrasts is
multivariate). doug On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
Hi Doug, Thanks for the response! Just out of curiosity, what map is typically
used
for group analyses? Should I have used a map other than sig on the
individual subject level as well?
Thanks! Alex
You'll have to run mri_vol2surf on each one separately to bring it into the fsaverage space, then mri_concat to stack all of the maps into one file. At that point you can compute a mean (also with mri_concat).
Generally, one does not do group analysis on sig maps though. doug
On 11/27/2012 05:08 PM, Alexandra Tanner wrote: > Hi Doug and Freesurfers, > I recently used mergecontrasts-sess to merge two contrasts of an
analysis
> in 50 different subjects. The command ran on each subject > individually > and > created a sig.nii and sig.ovpl file within a merged contrast folder
for
> each subject. I'd now like to look at an average map of the merged
contrasts across all 50 subjects.
> Does anyone know how to go about getting this average map for my group > of > 50 subjects? > Command I ran to get the sig.nii/sig.ovpl file for each subject:
mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction andor
> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix > 3 > pos 0 -map sig -sf > /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects
-df
> /cluster/roffman/users/Stable5_PerRun > Any help would be greatly appreciated! > Thanks,
> Alex
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/