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

[Renew Andrade]

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> 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 <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> Sent: Thursday, December 22, 2022 4:27 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         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 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> 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>  Sent: Tuesday, December 20, 2022 1:23 AM To: Huang, Yujing <yhuan...@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.   _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer   _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> . 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