External Email - Use Caution
Dear Yujing,
Thank you for your kind help (and sorry for my late reply).
It worked with the added flag; - measures thickness.
I appreciate your advice on adding directives at the end of the recon-all
command.
Best,
Asuka
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
Sent: 16 January 2024 13:41
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure
The command should look like this ‘recon-all -s subjid -qcache -all -i
input-file’
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Asuka Toyofuku
Sent: Monday, January 15, 2024 9:45 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure
External Email - Use Caution
Dear Yujing,
Thank you very much for your kind help.
So, you're saying I need more directive other than -qcashe?
My command was;
for d in Te* te* EPK* epk*
do recon-all -s $d -qcache
done
Do you think I should add another directive, such as -all or -autorecon-all?
So, the command line looks like this?
recon-all -s -subjid -qcashe - autorecon-all
I ran recon-all -qcashe not on the fsaverage folder, but in the SUBJECT_DIR.
In the previous post, I attached the wrong recon-all log (which was from
fsaverage>scripts folder), but now I'm attaching the recon-all log file from a
random subject folder.
Could you please look and check this recon-all as well?
Many thanks!
Best,
Asuka
________________________________
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 Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Sent: 12 January 2024 14:24
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure
Your recon-all command doesn’t have the directive to tell it what to run. You
also need to specify input files for your initial run. See this wiki page for
detail MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1WHtKoBRWRweL9tOk04WS_fJMQNq-6FmCk7jSMyjZxjX34yU-Dlr5b4MzSwJL0G4PCxBUEWet96Y3jjqc8Eg-MkfKhwWflyMuhk9fmnVywIMKVjjl3LCipveJDkFaKnkM_qJ3ZE4TUygho39aVC6uloeAdYv3L3E1RgcAfLZ66tZhKh6x41SPMkse4TUZNWr7qUY6z5ebLWoZYv8vnwoKlxK40EFn409Puic2n3fgLNZZOvEb99nWSNV3_rFb3lo7l29NkdLmDJzD7xafSmiEzetkbSw7Db1ENHv8B_2bVA5S5Zt2oBdDE8fBRfMMl4gs/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all<https://secure-web.cisco.com/11Bilsco5cPfi23kohUaJckmoejScJgxCVT9TueKMZWvsx7dAntYubRwWYXHtGKljKeBLeTqzQQ5UePuZUZnRFzxae5FFSuLRLH4HzelINkwLs96J8N2iaElEUM_9YKPg9etzBOD8OEAuG2UfdHxpyONcBHtLAn_f6EkrCSoSjzjNvXi_oX7KVCXXUF3o5g3Bjyz-ezPwcZ5YFtvqdbIYv52nG9qbUuOOaolTNutoq-ibvyTwQgNV48YK3yt4Hsi_B54h6NAIo1rBwTyHrWCfvL9-lF9ZVJPN9vRL5Pst33y1_GcnaQjVirIdC2QsnN3-/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all>
The recon-all.log attached contains runs between 2009 and 2010 on subject
‘fsaverage’.
‘fsaverage’ is an average subject comes with Freesurfer distribution in
$FREESURFER_HOME/subjects/. fsaverage is a template brain based on a
combination of 40 MRI scans of real brains. It can be used as a common space
for group comparison. You don’t want to run recon-all on it.
Your SUBJECTS_DIR should not set to your Freesurfer download/install directory.
Set it to some other directory where you have the write permission.
You should see ‘fsaverage’ as a symbolic link in your SUBJECTS_DIR.
Best,
Yujing
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 Asuka Toyofuku
Sent: Friday, January 12, 2024 4:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer recon-all qcache partial failure
External Email - Use Caution
Dear Freesurfer researchers,
I have an issue with recon-all-qcashe results. (please find the recon-all.log
attached.)
The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but
it did not create fsaverage files with different smoothing levels (e.g.,
lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh,
lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf"
folder.
I used the command below:
for d in Te* te* EPK* epk*
do recon-all -s $d -qcache
done
(Subjects names start from either Te, te, EPK or epk)
For several subjects with failed recon-all commands, I re-ran the command
individually:
recon-all -s subjectname -qcashe
(output from the terminal window)
It could also be that recon-all was running at one point but died in an
unexpected way.
If it is the case that there is a process running, you can kill it and start
over or just let it run.
If the process has died, you should type:
rm
/media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh
**Try to copy the line and then rerun again with the quche code.
I'm currently using
freesurfer-x86_64-redhat-linux-gnu-dev4-20090216.
Do you have any ideas why the command did not produce different fwhm files?
I'm thinking about re-running the recon-all again, so I would appreciate it if
you could help me modify the commands.
Thank you very much in advance.
Best regards,
Asuka
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