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
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Renew Andrade
Sent: Thursday, December 22, 2022 1:31 PM
To: Kumar, Avnish <avnish.ku...@mgh.harvard.edu>
Cc: Huang, Yujing <yhuan...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>; Dicamillo, Robert <rdicami...@mgh.harvard.edu>
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
<avnish.ku...@mgh.harvard.edu<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 <folder-name>
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
Sent: Thursday, December 22, 2022 11:59 AM
To: Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>;
Renew Andrade <andradere...@yahoo.com<mailto:andradere...@yahoo.com>>;
Dicamillo, Robert
<rdicami...@mgh.harvard.edu<mailto:rdicami...@mgh.harvard.edu>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<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 <andradere...@yahoo.com><mailto:andradere...@yahoo.com>
Sent: Thursday, December 22, 2022 4:27 AM
To: Huang, Yujing <yhuan...@mgh.harvard.edu><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
<yhuan...@mgh.harvard.edu<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 <andradere...@yahoo.com<mailto:andradere...@yahoo.com>>
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing <yhuan...@mgh.harvard.edu<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
<yhuan...@mgh.harvard.edu<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 <andradere...@yahoo.com<mailto:andradere...@yahoo.com>>
Sent: Tuesday, December 20, 2022 1:23 AM
To: Huang, Yujing <yhuan...@mgh.harvard.edu<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>
<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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