Hi Sue, that looks correct. I think it is an open question as to whether you should use the corrected maps or use the uncorrected and then correct the final map. Maybe someone else can chime in.
doug On 10/23/2013 09:49 AM, Susan Ruiz wrote: > Hi Doug, > > This is /very/ helpful. > > Procedurally, would this be the correct approach? > > For positive % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.pos.sig.cluster.nii > condBvFix.th3.pos.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.pos.sig.cluster.nii --i > condBvFix.th3.pos.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o positive.AvsB.nii > > For negative % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.neg.sig.cluster.nii > condBvFix.th3.neg.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.niigrf.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.neg.sig.cluster.nii --i > condBvFix.th3.neg.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o negative.AvsB.nii > > Note that for positive activation differences I would use sign=pos for > each condition vs fixation during mri_glmfit-sim, and for > "deactivation" clusters I use sign=neg for each condition vs fixation > during mri_glmfit-sim. BUT for both cases I use sign=pos for condition > A vs. condition B. > > Thanks so much! > > Best, > ~Sue > > > > On Tue, Oct 22, 2013 at 10:50 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > Hi Sue, I agree that they are not the same thing. There is not a > single > flag that will do what you want. What you are describing is a post-hoc > test. So you look for places where A != B, then within those > voxels you > do posthoc tests. You can implement this with a conjunction analysis > where you set up threeway conjunction A>B and A>0 and B>0. You can do > this with the --conjunt option to mri_concat > doug > > > On 10/21/2013 02:13 PM, Susan Ruiz wrote: > > Hi all, > > > > When running a functional analysis and comparing two experimental > > conditions, we observed that there are some voxels/vertices > where both > > condition A and condition B have a positive % signal change from > > baseline, and condition A has greater activity than condition B. > > > > In other regions, both condition A and condition B have negative % > > signal change from baseline, but condition B has a greater absolute > > value % signal change (thus relative to baseline condition B has > more > > "deactivation"--a term I am using since you all know what I mean > even > > if the term itself is imperfect). > > > > Since, in both cases, the % signal change is technically > condition A > > > condition B, the between-conditions maps do not distinguish > these two > > scenarios. FS-FAST sees these as being the same. Is there a way to > > tell FS-FAST to cluster these scenarios separately? Is there a > > compelling reason why I should not consider these different > > situations? It seems to me that the interpretation of what's taking > > place in these two scenarios is not identical. Agree or > disagree? Can > > FS-FAST distinguish these with a flag I don't know about? > > > > Thank you, > > ~Sue > > > > -- > > * * ** *** ***** ******** ************* > > Susan Mosher Ruiz, Ph.D. > > Research Scientist > > Boston University School of Medicine > > Laboratory of Neuropsychology > > VA Boston Healthcare System > > smos...@bu.edu <mailto:smos...@bu.edu> <mailto:smos...@bu.edu > <mailto:smos...@bu.edu>> > > * * ** *** ***** ******** ************* > > > > -- > Douglas N. 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