On 21 Dec 2022, at 20:17, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

Hi Rene,

 

I don’t see any errors in your recon-all log.

 

I’m wondering if ‘ln -sf’ works on Mac.

 

Can you try the following:

1. cd to ‘surf’ directory

2. ln -sf lh.pial.T1 testlink

3. ls -l testlink

4. ls -lt ?h.pial* ?h.white* ?h*.sphere.reg

 

Can you send the output from those commands?

 

Yujing

 

 

From: Renew Andrade <andraderenew@yahoo.com> 
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing <YHUANG43@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?

 

        External Email - Use Caution        

andraderenew@andraderenew:/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$

      ls -l lh.pial*

-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.pial.T1

 

 

 

This is all I have. Thanks for the help in advance. 

On 20 Dec 2022, at 15:12, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

 

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?

 

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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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