Sorry, I misread your previous email as "Indeed BPM does do Clusterwise
correction." instead of "Indeed BPM doesn't do Clusterwise correction."
The FWHM is the full-width-half-max and is a measure of the spatial
smoothness. This is always needed for cluster-wise correction. This is
usually obtained during the group analysis by examining the residuals,
so it should come out of what ever you are using for group analysis. If
it does not come out of BPM, then that is a problem that I cannot help
you with (talk to whoever programmed BPM).
doug
On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote:
Hello Douglas,
Sorry if I haven't been clear. I'm trying to explain my needs :
1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit
would do. However, outputs of this toolbox only give me beta maps and
uncorrected Tmaps.
2) With only these uncorrected Tmaps outputs, I'd like to apply
Clusterwise correction as mri_glmfit-sim would do with the same
arguments if possible (--cache ; --cwp ; --2spaces ; ...).
--> Is there a way to succeed in 2) with some manual scripting ?
--> Is the mri_volcluster adapted as you proposed : in this case you
said I need to know the FWHM of my BPM analysis, how could I obtain this ?
--> Would I have access in this way to arguments --cache and --cwp as
used in mri_glmfit-sim ?
I hope I have been clearly.
Thanks in advance for guiding me !
Best regards,
Matthieu
2015-04-15 3:06 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>:
I guess I don't understand what you are asking for. If BPM outputs
a cluster-corrected volume, then why can't you just map that to
the surface and be done with it?
On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:
Hello Douglas,
Indeed BPM doesn't do Clusterwise correction.
What does the FWHM of the BPM analysis correspond to ? And how to
find it ?
Manu thanks !
Best regards,
Matthieu
Le 15 avr. 2015 00:23, "Douglas Greve" <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>> a écrit :
So BPM does not do clusterwise correction? You could use
mri_volcluster, but you'll need to know the FWHM of your BPM
analysis
doug
On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:
Dear FreeSurfer's experts,
For personnal need I use the BPM toolbox (Biological
Parametric Mapping) to compute GLM analysis. The outputs of
this Toolbox gave me beta maps and Tmaps.
However, precedently I used the whole FreeSurfer group
analysis tutorial on other datas, including the Clusterwise
Correction for multiple comparisons. And now in order to
compare results, I'd like to use this Clusterwise Correction
consequently to my BPM Toolbox GLM analysis.
Is it possible to manually adapt some scripts ? In this way,
how could I upgrade my outputs to these of "mri_glmfit" in
order to launch Clusterwise Correction after ?
Many thanks in advance for helping !
Best regards,
Matthieu
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