Hi,
That's a good question. I have no idea why changing only the contrast
(and changing nothing anatomical) should result in the smoothing being
different. I also learned that previous research assistants in our lab
encountered the same exact issue but they didn't solve it. My best
guess is it is that some randomness that results from average7 being
incompatible with an operation along the stream, either in stxgrinder,
mris_preproc, or mri_glmfit.
Thanks,
Rob
Doug Greve wrote:
If the simulation command-line would be the same across the different
contrasts and the contrast matrices have the same number of rows, then
you do not have to redo the simulation. Why is the smoothing changing
if you are using the same fsgd file?
Robert Levy wrote:
Hi Doug,
As you suggested, I ran mc simulation data with a threshold taken
from fwhm.dat so that the smoothing on the simulation matches the
smoothing on the real data. What I was wondering is, if I use the
same simulation data for several contrasts (they have the same fsgd,
so this seems like a valid thing to do), it becomes less clear how to
choose the smoothing. Or maybe it is not possible to use the same mc
simulation data, because the smoothing turns out to be different.
Should I instead use an average of the smoothing values, or maybe use
the lowest one? Conceptually it seems like this might make the
results less accurate, but in practice is there a certain level of
slack in smoothing without sacrificing accuracy? If not, it makes a
big difference, because the full simulation will take 6 days instead
of 2. The z simulation, which at at least with the level of
smoothing we have applied, showed results being much less
significant, which is why I'm trying the full mc simulation.
Thanks,
Rob
Just to give you an idea of the variance in the smoothing reported in
fwhm.dat for the three contrasts:
lh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 17.128043
rh.ASvfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 16.675573
lh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.202638
rh.ASevASc_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.771982
lh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 14.438915
rh.ASevfix_8s_BwGroupError5.fsfast.glmdir/fwhm.dat 15.766636
--
Robert P. Levy, B.A.
Research Assistant, Manoach Lab
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St., Room 2656
Charlestown, MA 02129
email: [EMAIL PROTECTED]
phone: 617-726-1908
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
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