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 >>>>>> 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/ >> >> >> > > >
-- 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.
