[Freesurfer] GLM fitting for the cortical volume

[Ali Radaideh]

Dear FS experts,

I have managed to run the *glm_fit* on the cortical thickness and area on a
group of MS patients. However, i am not sure how to do this on the cortical
volume. which file represents the cortical volume in subject's directory?

Many thanks,

-- 







*Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of
the Faculty of Allied Health SciencesThe Hashemite University, Zarqa,
JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo *
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
*
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Re: [Freesurfer] slips on the 3D surface

[Bruce Fischl]

Hi Michael

I wouldn't worry about those tiny bumps, particularlly as they are 
typically not in cortical regions

cheers
Bruce
On Fri, 23 Jun 2017, Michael Davies wrote:

> 
> Hello, i have noticed a blip or two on a few of my inflated 3D surfaces and 
> have not been able to edit them away as yet. I have made manual adjustments 
> to the pial boundaries,
> intensity normalization and wm volume in the 2D surface stage but none of 
> these correct the problem after running recon-all. Do you have any 
> suggestions as to how to correct
> this problem please? [IMAGE]
> Kind regards, Michael
> 
> 
>
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[Freesurfer] How to obtain MNI coordinates

[AKUDJEDU, THEOPHILUS]

Hi All,

I am trying to visualise nodes of a brain network reconstructed using 
FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain 
Net Viewer and Network Based Statistics software.
In order to do so, I need to upload a .txt file listing Freesurfer labels 
coordinates in MNI space. Is there any way I can get a list of MNI coordinates 
for my set of labels?

Many thanks,
Theo




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