Re: [Freesurfer] [martinos-tech] FSFAST between-conditions contrasts

correct

On 12/04/2013 01:40 PM, Susan Ruiz wrote:

Hi Doug,

Thanks. Just to confirm, for the negative-only maps, I assume I would set max = -2 in mni_binarize, e.g.:

mri_binarize --i condAvfix.sig.mgh --max -2 --o condAvfix.sig.neg.mask.mgh mri_binarize --i condBvfix.sig.mgh --max -2 --o condBvfix.sig.neg.mask.mgh

Is that correct?

~Sue

On Wed, Dec 4, 2013 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

you would create a mask from the uncorrected results, eg,

mri_binarize --i condAvfix.sig.mgh --min 2 --o condAvfix.sig.mask.mgh
mri_binarize --i condBvfix.sig.mgh --min 2 --o condBvfix.sig.mask.mgh
fscalc condAvfix.sig.mask.mgh and condBvfix.sig.mask.mgh - o
condA-and-Bvfix.sig.mask.mgh

The mri_binarize commands mask to anything with a sig>2 (so
positive only)

Then run mri_glmfit on condAvcondB and using
condA-and-Bvfix.sig.mask.mgh as the mask (--mask), then run
mri_glmfit-sim on that analysis. Note that you will have to rerun
the simulation because the search space will have changed.

doug


On 12/03/2013 12:05 PM, Susan Ruiz wrote:

    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 <mailto:greve@nmr.mgh.harvard.edu>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto: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>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>
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    <mailto:greve@nmr.mgh.harvard.edu>

            <mailto: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
                >
                > --
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                > Susan Mosher Ruiz, Ph.D.
                > Research Scientist
                > Boston University School of Medicine
                > Laboratory of Neuropsychology
                > VA Boston Healthcare System
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