Hi Rene,

Can you send your recon-all.log? It is in the ‘scripts’ directory. 

‘lh.pial’ should be created as a link to ‘lh.pial.T1’ if you are not processing T2/FLAIR.  If you go ‘surf’ directory, do ‘ls -l lh.pial*’, what does it shows?

Best,

Yujing

From: Renew Andrade <andraderenew@yahoo.com>
Sent: Tuesday, December 20, 2022 1:23 AM
To: Huang, Yujing <YHUANG43@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?

        External Email - Use Caution        

Dear Yujing:

I wasn’t aware that there was an answer to my email that’s the reason it took me a while to write back. But I answer here. 

Yes I mean lh.pial.T1. I don’t have any other lh.pial. The recon-all command is properly correct like recon-all -all -i -s -openmp 8. Yes the freesurfer version is 7.1.1. 

Best, 

Rene Andrade. 

Hi Rene,
 
Do you mean lh.pial.T1? Do you have any other lh.pial* files in the directory?
What is your recon-all command line? And can you also provide the Freesurfer 
version you are running?
 
Best,
 
Yujing
 
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Renew Andrade
Sent: Tuesday, December 13, 2022 7:24 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] lh.pial lh.pialT1n same file?
 
        External Email - Use Caution        
 
Dear experts:
 
I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have 
lh.pial is that an error from recon-all? Should I rerun recon-all. Or just 
autorecon-pial? Would that change anything?
 
Best, 
Rene Andrade. 
 
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