did you try looking in the output to see if those files are actually there?

On 2/13/19 1:11 PM, Zhi Li wrote:
>
>         External Email - Use Caution
>
> Hello FreeSurfer experts,
>
> I am trying recon-all in a SGE cluster. However, the size of of the
> results was smaller than that executed in a local CentOs system. I did
> not found error in the recon-all log file which ended with "recon-all
> -s sub001 finished without error". But when I used QAtools, it reported:
>
>      Checking if all files exist...FAILED
>      (read ../a003/scripts/recon_checker.log)
>      ERROR: Subject a003 missing output file
> ../mri/transforms/talairach.m3z.inv.x.mgz
>      ERROR: Subject a003 missing output file
> ../mri/transforms/talairach.m3z.inv.y.mgz
>      ERROR: Subject a003 missing output file
> ../mri/transforms/talairach.m3z.inv.z.mgz
>      ERROR: Subject a003 missing output file ../mri/nu_noneck.mgz
>      ERROR: Subject a003 missing output file ../label/lh.BA1.label
>      ERROR: Subject a003 missing output file ../label/lh.BA2.label
>      ERROR: Subject a003 missing output file ../label/lh.BA3a.label
>      ERROR: Subject a003 missing output file ../label/lh.BA3b.label
>      ERROR: Subject a003 missing output file ../label/lh.BA4a.label
>      ERROR: Subject a003 missing output file ../label/lh.BA4p.label
>      ERROR: Subject a003 missing output file ../label/lh.BA6.label
>      ERROR: Subject a003 missing output file ../label/lh.BA44.label
>      ERROR: Subject a003 missing output file ../label/lh.BA45.label
>      ERROR: Subject a003 missing output file ../label/lh.V1.label
>      ERROR: Subject a003 missing output file ../label/lh.V2.label
>      ERROR: Subject a003 missing output file ../label/lh.MT.label
>      ERROR: Subject a003 missing output file ../label/lh.BA.annot
>      ERROR: Subject a003 missing output file ../stats/lh.BA.stats
>      ERROR: Subject a003 missing output file ../label/rh.BA1.label
>      ERROR: Subject a003 missing output file ../label/rh.BA2.label
>      ERROR: Subject a003 missing output file ../label/rh.BA3a.label
>      ERROR: Subject a003 missing output file ../label/rh.BA3b.label
>      ERROR: Subject a003 missing output file ../label/rh.BA4a.label
>      ERROR: Subject a003 missing output file ../label/rh.BA4p.label
>      ERROR: Subject a003 missing output file ../label/rh.BA6.label
>      ERROR: Subject a003 missing output file ../label/rh.BA44.label
>      ERROR: Subject a003 missing output file ../label/rh.BA45.label
>      ERROR: Subject a003 missing output file ../label/rh.V1.label
>      ERROR: Subject a003 missing output file ../label/rh.V2.label
>      ERROR: Subject a003 missing output file ../label/rh.MT.label
>      ERROR: Subject a003 missing output file ../label/rh.BA.annot
>      ERROR: Subject a003 missing output file ../label/BA.ctab
>      ERROR: Subject a003 missing output file ../stats/rh.BA.stats
>      ERROR: Subject a003 missing output file
> ../stats/lh.entorhinal_exvivo.stats
>      ERROR: Subject a003 missing output file
> ../stats/rh.entorhinal_exvivo.stats
>
> In addition, the QA results were black. But if I apply QATools on
> these results in a local CentOs system, the results seemed normal.
> Should this QA problem be caused by X11? I did not install FSL in the
> SGE cluster, would this be the problem of missing files after
> recon-all? Any suggestions would be appreciated.
>
> Thanks and best wishes,
>
> Lizhi
>
>
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