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