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/