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Thank you so much! I just sent the gzipped subject directory subjectdir.gz. 
My main concern is that a lot of the lateral gray matter isn't included. Here are some Talairach coordinates that illustrate the areas I'm concerned about: (-67 -27 -9) (-65 -33 22). 

Let me know if it didn't send properly or if I can do anything else. 

Thanks again,
Monica

On Fri, Jan 31, 2020 at 10:34 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Monica

sure, if you tar and gzip the entire subject dir and ftp it to us, then
send us a description that includes the voxel coords of where you think
things should be more accurate we will take a look

cheers
Bruce
On Fri, 31 Jan 2020,
Monica Bondy wrote:

>
>         External Email - Use Caution        
>
> Dear Freesurfer experts,
> I was wondering if I could get some help with a problem that I keep
> experiencing. For some of the patients, their gray matter is not properly
> included in the pial surface. I have tried tkmregister and using control
> points but neither have been successful. 
> I have read on a separate thread that editing the wm.mgz may be helpful but
> could I have some guidance on this please? Also, I know it can be difficult
> to tell the problem based on the description so please let me know if I can
> send something over to help. I'm still very much learning how to work
> freesurfer so I really appreciate your help. 
> (Note: I am using version 5.3) 
>
> Thank you,
> Monica 
>
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