[Freesurfer] Beta extraction

[Jahan, Bushra]

I am wondering how to extract beta values from the clusters of task functional 
data, particularly output of the multiple comparisons correction?

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

[Freesurfer] Cortical & subcortical cluster size

[Jahan, Bushra]

Hi,


I'm wondering which column in the FreeSurfer summary file represents the 
cluster size for the cortical and subcortical clusters.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Beta extraction

[Jahan, Bushra]

When I ran the following command (with our data), I got the average beta values 
for each segmentation i.e. only 5 beta values (as opposed to 5 beta values for 
each subject).


mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
beta.clusters.dat


That said, is it necessarily to run the previous command for each subject  (in 
order to extract 5 beta values for each subject) or is there way to extract 
betas for each subject from the group analysis?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Thursday, November 29, 2018 11:19:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Beta extraction

Use something like
mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
beta.clusters.dat

See mri_glmfit-sim --help for more info on the OCN file and mri_segstats
--help for info on the avgwf file


On 11/29/2018 04:40 PM, Jahan, Bushra wrote:
> I am wondering how to extract beta values from the clusters of task
> functional data, particularly output of the multiple comparisons
> correction?
>
> Aava Jahan
>
>
> ___
> 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] Beta Extraction

[Jahan, Bushra]

When I ran the following command (with our data), I got the average beta values 
for each segmentation i.e. only 5 beta values (as opposed to 5 beta values for 
each subject).


mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
beta.clusters.dat


That said, is it necessarily to run the previous command for each subject  (in 
order to extract 5 beta values for each subject) or is there way to extract 
betas for each subject from the group analysis?

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

[Freesurfer] (no subject)

[Jahan, Bushra]

Hello - I'm wondering how to generate a label in FreeSurfer from peak 
activation in a cluster? Is there a specific command?
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Creating Labels

[Jahan, Bushra]

Hello,

I am wondering how to generate a label in FreeSurfer from peak activation in a 
cluster - is there a specific command?

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