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 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Thursday, December 22, 2022 11:59 AM To: Huang, Yujing <yhuan...@mgh.harvard.edu>; Renew Andrade <andradere...@yahoo.com>; Dicamillo, Robert <rdicami...@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 <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? 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