Hi Doug,

thank you very much!

I have two follow-up questions for your two suggestions:

1) If I want to use mri_glmfit-sim but my conjunctions are not from contrasts that are all from the same GLM, I guess I can still do what you suggested but I will have to come up with a fwhm.dat for the conjunction, correct?

Is there a way to compute this from the conjunction sig map, or should I use the average or the max or the min of the contrasts that go into the conjunction? This is for functional data.

2) It seems that there is a version of mri_mcsim that allows one to specify a range of FWHM with the flag --fwhm-max; however, version 1.17 that comes with the 5.1 and 5.3 releases does bot have that option. Is the version of mri_mcsim that understands --fwhm-max available?

Thanks again, Caspar

2013/10/24 Douglas N Greve <greve@nmr.mgh.harvard.edu>

Hi Caspar, there are a couple of things you can do:

1. Go into the mri_glmfit folder used to create the input contrasts to
the conjunction. Create a subfolder. Save the conjunction as sig.mgz and
create a file called "C.dat" (it can be empty) in this folder. Then run
mri_glmfit-sim specifying to do the simulation rather than using cached
data.

2. Create cached data by running mri_mcsim. This may take longer than
#1, but once you have the cached data you do not need to run it again,
which could be useful if you are going to do more analyses with this
template

doug

On 10/23/2013 02:55 PM, Caspar M. Schwiedrzik wrote:
> Hi,
> I have a question regarding cluster size thresholding using
> mri_glmfit-sim. Namely, I have a sig.nii conjunction map that I made
> with mri_concat.
> The analyses that serve as input to the conjunction map are done on a
> custom surface template.
> If I want to run mri_glmfit-sim, how would that work? I obviously do
> not have precached data.
> Thanks, Caspar
>
>
>
>

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