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 https://surfer.nmr.mgh.harvard.edu/fswiki/recon-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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Friday, January 12, 2024 4:31 AM To: 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