: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Clusterwise Correction for Multiple Comparisons
Can you send your full mri_glmfit-sim command line? It looks like you used a
cluster forming threshold (CFT) of 1.3. If so, when you look at the uncorrected
sig.mgh files and threshold at
Can you send your full mri_glmfit-sim command line? It looks like you
used a cluster forming threshold (CFT) of 1.3. If so, when you look at
the uncorrected sig.mgh files and threshold at 1.3, do you see the same
thing? Also, what is the threshold for the image below
On 3/1/2021 1:35 PM, Weera
If it is only one space, then you can just leave off --3spaces
On 9/3/19 1:48 PM, Gwang-Won Kim wrote:
>
> External Email - Use Caution
>
> Hi there,
> To perform a cluster-wise correction for multiple comparisons, I ran
> monte carlo simulation as follows: mri_glmfit-sim --glmdir g1v2.wl
Thank you Douglas !
Matthieu
2015-04-13 22:13 GMT+02:00 Douglas N Greve :
> clusterwise correction is a type of FWE correction. If the FWE you are
> using is good enough for you and you want to visualize the results on a
> surface, then use mri_vol2surf. If this was done on the SPM template
> sp
clusterwise correction is a type of FWE correction. If the FWE you are
using is good enough for you and you want to visualize the results on a
surface, then use mri_vol2surf. If this was done on the SPM template
space, then run the SPM T1 template through recon-all to get the surfaces
On 0
By the mean of SPM, the Biological Parmatring toolbox can do the FWE
correction and give me results on a glass brain. But I don't have any
cluster wise corrected P-maps on output.
Or did I miss something ?
Best regards,
Matthieu
2015-04-13 16:51 GMT+02:00 Douglas Greve :
> Does the BPM toolbo
Does the BPM toolbox (what's that?) not give you cluster correction? You
can try using mri_volcluster with the --grf option, but you'll need to
know the FWHM. Afterwards you can map the result to the surface
On 4/13/15 10:46 AM, Matthieu Vanhoutte wrote:
Hello Douglas,
Thanks but even if I do
Hello Douglas,
Thanks but even if I do the clusterwise correction in the volume, I can't
get an clusterwise corrected output volume image. The only things I have
are the Tmaps that I can threshold if wanted.
And I would like to project on fsaverage surface the results of the
clusterwise correctio
If you did the analysis in the volume, then you have to do the
clusterwise correction in the volume.
On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote:
Dear experts,
I had to make volumic statistical analysis for the need to use BPM
toolbox. So, I got in the output of this statistical analysis som
It does not seem like it should take that much time. You might try this
program
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mcsim.linux
This is what I use to create the cached results that we distribute. You
can use the cached results unless you have a different mask. If y
Looks like it did not find any vertices above the threshold that you
used for the simulation (though it should give a better error msg).
Before you run the simulation, you can look at the map at your given
threshold. If there are no vertices above threshold, then nothing is
going to show up in
Thank you for your help. As regards to the display, I am using the command
that is found in the mri_glmfit-sim documentation. Even with that command I
don't see the display as it is shown in the documentation. In addition to
showing the clusters (all of them), the display also shows what looks l
It is for the whole brain. Not sure what you display command is, but
mri_surfcluster will save all clusters in the cwp map. You can then set
the tksurfer threshold to exclude the ones below your target sig level.
doug
Devdutta W wrote:
Hi,
In the mri_glmfit-sim command, when it does a "cluste
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