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<mailto:greve@nmr.mgh.harvard.edu
On Thu, Oct 24, 2013 at 11:36 AM, Douglas N Greve <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:smosher@bu.edu <mailto:smosher@bu.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>>
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--
* * ** *** ***** ******** *************
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Research Scientist
Boston University School of Medicine
Laboratory of Neuropsychology
VA Boston Healthcare System
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* * ** *** ***** ******** *************
--
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