Are you asking how to do subcortical analysis or are you asking how to account for subcortical analysis during correction for multiple corrections? For the latter, use --3spaces

On 3/12/2020 2:03 PM, Hengameh Marzbani wrote:

        External Email - Use Caution        

thank you for your detailed and helpful explanation.

question 3: I mean just left and right. But what should I do if I want to consider subcortical as well as left and right? 

Best Regards

Hengameh

On Thu, Mar 12, 2020 at 12:07 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

On 3/11/2020 4:21 PM, Hengameh Marzbani wrote:

        External Email - Use Caution        

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?

You can, the easiest way is to run mri_glmfit-sim and it will give you a list of clusters in a text file. If you set the cwp to 1, then it will give you all the clusters. See the help.

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?

Whole brain meaning left, right, and subcort or just left and right? If just left and right, then use --2spaces

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?

Demeaning makes the design matrix better conditioned. But also if you are looking at the difference in average thickness between two groups regressing out, eg, age, then simply using age as a regressor will reduce the efficiency of the estimation because the age itself will have a non-zero mean, so the regression is left trying to figure out what part of the thickness average is due to the group and what part is due to age.

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
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer