subject:"\[Freesurfer\] lh.pial lh.pialT1n same file\?"

Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-22 Thread Huang, Yujing

You can create the links if you are now working on ubuntu.

rh.pial -> rh.pial.T1 (ln -sf rh.pial.T1 rh.pial)
lh.pial -> lh.pial.T1
rh.fsaverage.sphere.reg -> rh.sphere.reg
lh.fsaverage.sphere.reg -> lh.sphere.reg
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


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Renew Andrade
Sent: Thursday, December 22, 2022 1:31 PM
To: Kumar, Avnish 
Cc: Huang, Yujing ; Freesurfer support list 
; Dicamillo, Robert 
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?


External Email - Use Caution
I am afraid the links didn’t survive the copy and can’t be undone because they 
were deleted from Mac when copied to the disc where they are used later on in 
ubuntu. Thank you all for the help. Then shall I create a copy of all those 
files missing as suggested by Yujing.

Eg rh.fsaverage.sphere.reg

And

Rh.white.preaparc.K

???


On 22 Dec 2022, at 19:08, Kumar, Avnish 
mailto:avnish.ku...@mgh.harvard.edu>> wrote:
If you want your links to also be copied over in Linux/Mac you can use the --a 
argument with the cp command:
cp --a 

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Thursday, December 22, 2022 11:59 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>; 
Renew Andrade mailto:andradere...@yahoo.com>>; 
Dicamillo, Robert 
mailto:rdicami...@mgh.harvard.edu>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?

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 <mailto:andradere...@yahoo.com>
Sent: Thursday, December 22, 2022 4:27 AM
To: Huang, Yujing <mailto:yhuan...@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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 andrade

Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-22 Thread Renew Andrade

External Email - Use CautionI am afraid the links didn’t survive the copy and can’t be undone because they were deleted from Mac when copied to the disc where they are used later on in ubuntu. Thank you all for the help. Then shall I create a copy of all those files missing as suggested by Yujing. Eg rh.fsaverage.sphere.reg And Rh.white.preaparc.K??? On 22 Dec 2022, at 19:08, Kumar, Avnish  wrote:





If you want your links to also be copied over in Linux/Mac you can use the --a argument
 with the cp command:
cp
 --a 


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Douglas N. Greve 
Sent: Thursday, December 22, 2022 11:59 AM
To: Huang, Yujing ; Renew Andrade ; Dicamillo, Robert 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?
 

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 
 
Sent: Thursday, December 22, 2022 4:27 AM
To: Huang, Yujing 

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 <yhuan...@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 <andradere...@yahoo.com> 
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing <yhuan...@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 an

Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-22 Thread Kumar, Avnish

If you want your links to also be copied over in Linux/Mac you can use the --a 
argument with the cp command:
cp --a 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, December 22, 2022 11:59 AM
To: Huang, Yujing ; Renew Andrade 
; Dicamillo, Robert 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?

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 <mailto:andradere...@yahoo.com>
Sent: Thursday, December 22, 2022 4:27 AM
To: Huang, Yujing <mailto:yhuan...@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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 
mailto:yhuan...@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 mailto:andradere...@yahoo.com>>
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Hi Rene,

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

‘lh.pial’ s

Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-22 Thread Douglas N. Greve

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 
*Sent:* Thursday, December 22, 2022 4:27 AM
*To:* Huang, Yujing 
*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 
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 
*Sent:*Tuesday, December 20, 2022 11:04 AM
*To:*Huang, Yujing 
*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
 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 
*Sent:*Tuesday, December 20, 2022 1:23 AM
*To:*Huang, Yujing
;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

Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-22 Thread Huang, Yujing

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 
Sent: Thursday, December 22, 2022 4:27 AM
To: Huang, Yujing 
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 
mailto:yhuan...@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 mailto:andradere...@yahoo.com>>
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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 
mailto:yhuan...@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 mailto:andradere...@yahoo.com>>
Sent: Tuesday, December 20, 2022 1:23 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>; 
freesurfer@nmr.mgh.harvard.edu<mailto: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 comman

Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-22 Thread Renew Andrade

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  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 mailto:andradere...@yahoo.com>> 
> Sent: Tuesday, December 20, 2022 11:04 AM
> To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
> Cc: freesurfer@nmr.mgh.harvard.edu <mailto: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  <mailto:yhuan...@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 mailto:andradere...@yahoo.com>> 
> Sent: Tuesday, December 20, 2022 1:23 AM
> To: Huang, Yujing  <mailto:yhuan...@mgh.harvard.edu>>; freesurfer@nmr.mgh.harvard.edu 
> <mailto: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 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto: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 <mailto: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 f

Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-21 Thread Huang, Yujing

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 
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing 
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 
mailto:yhuan...@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 mailto:andradere...@yahoo.com>>
Sent: Tuesday, December 20, 2022 1:23 AM
To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>; 
freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto: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<mailto: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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Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-20 Thread Huang, Yujing

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 
Sent: Tuesday, December 20, 2022 1:23 AM
To: Huang, Yujing ; 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

mailto: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<mailto: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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Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-19 Thread Renew Andrade

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 
 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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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] lh.pial lh.pialT1n same file?

2022-12-13 Thread Huang, Yujing

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 
 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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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] lh.pial lh.pialT1n same file?

2022-12-13 Thread Renew Andrade

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. 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

Re: [Freesurfer] lh.pial lh.pialT1n same file?

[Freesurfer] lh.pial lh.pialT1n same file?

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