yes, you can copy that. I'm cc'ing Rob in case he has any insights. @ Renew, you should try running the whole recon-all in a single platform. If you copied it from Mac to ubuntu, it is possible that those links weren't created in Mac or did not survive the copy.

On 12/22/2022 10:28 AM, Huang, Yujing wrote:

Hi Rene,

From your recon-all.log, I see you ran freesurfer-darwin-macOS-7.1.1-20200811-8b40551 on your MacBook:

BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: root Machine: Renes-MacBook-Air.local Platform: Darwin PlatformVersion: 21.6.0 CompilerName: Clang CompilerVersion: 10.0.1

It looks like recon-all failed to create these links in ‘surf’ directory because of the permission issues:

rh.pial -> rh.pial.T1

lh.pial -> lh.pial.T1

rh.fsaverage.sphere.reg -> rh.sphere.reg

lh.fsaverage.sphere.reg -> lh.sphere.reg

I think you can copy in these files for now

cp rh.pial.T1 rh.pial

cp lh.pial.T1 lh.pial

cp rh.sphere.reg rh.fsaverage.sphere.reg

cp lh.sphere.reg lh.fsaverage.sphere.reg

Doug, can you confirm that?

Also, I can’t tell from recon-all script if in 7.1.1, we create these links?

rh.white.K -> rh.white.preaparc.K

rh.white.H -> rh.white.preaparc.H

lh.white.K -> lh.white.preaparc.K

lh.white.H -> lh.white.preaparc.H

Best,

Yujing

From: Renew Andrade <andraderenew@yahoo.com>
Sent: Thursday, December 22, 2022 4:27 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

Hi Yujing

I’m using this in ubuntu I don’t remember if I did recon-all in Mac and may be that’s why you are assuming I’m working on Mac.

Anyways ln -sf works as I am in ubuntu.

The problem is as you will see there seems to be an issue with permission even with sudo.

So ls -l testlink I din’t try as I couldn’t do any symbolic link.

Best,

Rene.
surfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$ sudo ln -sf lh.pial.T1 testlink

ln: failed to create symbolic link 'testlink': Operation not permitted

(base) andraderenew@andraderenew:/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$ ls -lt ?h.pial* ?h.white* ?h*.sphere.reg

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

-rwxr-xr-x 1 andraderenew andraderenew 4553578 ago 23 03:05 lh.sphere.reg

-rwxr-xr-x 1 andraderenew andraderenew 505671 ago 23 03:05 lh.white.preaparc.H

-rwxr-xr-x 1 andraderenew andraderenew 502915 ago 23 03:05 rh.white.preaparc.H

-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.pial.T1

-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.white.preaparc

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

-rwxr-xr-x 1 andraderenew andraderenew 4528774 ago 23 03:05 rh.sphere.reg

-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.white

-rwxr-xr-x 1 andraderenew andraderenew 505671 ago 23 03:05 lh.white.preaparc.K

-rwxr-xr-x 1 andraderenew andraderenew 502915 ago 23 03:05 rh.white.preaparc.K

-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.white.preaparc
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?

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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