2013/10/30 Douglas N Greve <greve@nmr.mgh.harvard.edu>

what OS platform are you using?

On 10/30/2013 11:00 AM, Caspar M. Schwiedrzik wrote:

Hi Doug,

thanks for the advice.
When I try to use the new mri_mcscim, I get the following error messages:
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found
/usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found
/lib64/libc.so.6: version `GLIBC_2.7' not found
Caspar

2013/10/30 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

On 10/30/2013 08:51 AM, Caspar M. Schwiedrzik wrote:

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.

If they are not from the same GLM, then I would use the larger of
the two FWHMs.

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?

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

Thanks again, Caspar

2013/10/24 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>>>

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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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