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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, December 22, 2022 11:59 AM To: Huang, Yujing YHUANG43@mgh.harvard.edu; Renew Andrade andraderenew@yahoo.com; Dicamillo, Robert RDICAMILLO@mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu 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 andraderenew@yahoo.commailto:andraderenew@yahoo.com Sent: Thursday, December 22, 2022 4:27 AM To: Huang, Yujing YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.commailto:andraderenew@yahoo.com> Sent: Tuesday, December 20, 2022 11:04 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Cc: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.commailto:andraderenew@yahoo.com> Sent: Tuesday, December 20, 2022 1:23 AM To: Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Renew Andrade
Sent: Tuesday, December 13, 2022 7:24 AM
To: freesurfer@nmr.mgh.harvard.edumailto: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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