Re: [Freesurfer] Missing files after recon-all

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Yes I checked but these files are not there. I only found 'talairach.m3z' under '/mri/transforms' and some label files end with 'exvivo.label' under '/label', such as 'lh.BA1_exvivo.label' and 'lh.BA1_exvivo.thresh.label'.

Thanks and best wishes,

Lizhi

On Thu, 14 Feb 2019 at 13:43, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

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:

...

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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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