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>

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    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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* * ** *** ***** ******** *************
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>
* * ** *** ***** ******** *************
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--
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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
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Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




--
* * ** *** ***** ******** *************
Susan Mosher Ruiz, Ph.D.
Research Scientist
Boston University School of Medicine
Laboratory of Neuropsychology
VA Boston Healthcare System
smosher@bu.edu
* * ** *** ***** ******** *************