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 >>>>> gr...@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 >>> gr...@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 > gr...@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/ > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
