Hi Doug,
I have been running this analysis as I described in my previous email by clustering pos and neg activation separately using glmfit-sim for condAvfix, condBvfix, and condAvcondB, and then making conjunction maps. It occurred to me that you had mentioned in your response that is might be possible to use the *uncorrected* maps first and then cluster-correct the final conjunction map. However, I cannot find a way to get pos-only or neg-only sig maps without running glmfit-sim. Is there a way to make pos-only sig maps or neg-only sig maps with just mri_glmfit? If so, how?? I can only identify how to do that with mri_glmfit-sim. Can I set mri_glmfit-sim to some parameters that will essentially make them uncorrected but still segregate pos and neg activation?
Thanks so much, ~Sue
On Thu, Oct 24, 2013 at 11:36 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
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 < greve@nmr.mgh.harvard.edu mailto:greve@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 > smosher@bu.edu <mailto:smosher@bu.edu> <mailto:smosher@bu.edu <mailto:smosher@bu.edu>> > * * ** *** ***** ******** ************* > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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. ------------------------------------ Yahoo! Groups Links <*> To visit your group on the web, go to: http://groups.yahoo.com/group/martinos-tech/ <*> Your email settings: Individual Email | Traditional <*> To change settings online go to: http://groups.yahoo.com/group/martinos-tech/join (Yahoo! ID required) <*> To change settings via email: martinos-tech-digest@yahoogroups.com <mailto:martinos-tech-digest@yahoogroups.com> martinos-tech-fullfeatured@yahoogroups.com <mailto:martinos-tech-fullfeatured@yahoogroups.com> <*> To unsubscribe from this group, send an email to: martinos-tech-unsubscribe@yahoogroups.com <mailto:martinos-tech-unsubscribe@yahoogroups.com> <*> Your use of Yahoo! Groups is subject to: http://info.yahoo.com/legal/us/yahoo/utos/terms/--
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