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.com Sent: Tuesday, December 20, 2022 11:04 AM To: Huang, Yujing YHUANG43@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 <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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