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Thank you for the quick response.

question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). I can see the clusters by tksurfer. But, Can I have a text file included all clusters?

question 3: I want to do the analyse by considering the whole brain. Is correct to use --2spaces? and also I I want to visualize the results in both hemisphere simultaneously. is it possible by freeview?

question 5: I can't understand what is the reason of using demean and normalize. Would you mind explaining to me? And when is it necessary to use them?

Thank you so much.
Hengameh

On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:


On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
>
>         External Email - Use Caution
>
> Hello Freesurfer developers,
> 1- I want to extract the uncorrected clusters from the uncorrected significance maps obtained from mri_glmfit for structural data (to illustrate cluster, size, location, and significance) like abs.sig.cluster.summary (summary of clusters (text))which is obtained from mri_glmfit-sim. Is there a way to do this?
Set the clusterwise p-value thresh to 1 (--cwp 1)
> 2- I don't see any clusters when I use cluster-based correction for multiple comparisons (for example mri_glmfit-sim \  --glmdir lh.Area.glmdir \ --sim mc-z 10000 2 mc-z.abs\ --sim-sign abs --cache 4 neg \  --cwp  0.05\  --2spaces). How much is it significant if I report the uncorrected clusters?
Usually, reveiewers won't let you report exclusivly uncorrected results.
> 3- Are there new ways of looking at the whole brain together (not left and right hemisphere separately)by Qdec and FSGD?
You can load both hemispheres into freeview, if that is what you mean
> 4- How can I do fdr correction in mri_glmfit-sim? what flag should I use?
You can't, use mri_fdr. Run with --help to get docs
> 5- How can I demean and normalize the covariates when I use FSGD? what flag should I use?
Add these lines in your FSGD file
DeMeanFlag 1
ReScaleFlag 1
>
> Thanks you in advance!
> Best regards,
> Hengameh
>
>
>
>
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