Missing files after recon-all

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Re: [Freesurfer] dt_recon issue

Zhi Li

13 Feb 2019 13 Feb '19

1:11 p.m.

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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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Greve, Douglas N.,Ph.D.

14 Feb 14 Feb

1:42 p.m.

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Zhi Li

2:55 p.m.

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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:

...
    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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Greve, Douglas N.,Ph.D.

3:27 p.m.

can you send the recon-all.log file?

On 2/14/19 2:55 PM, Zhi Li wrote:

...

External Email - Use Caution

Thanks and best wishes,

Lizhi

On Thu, 14 Feb 2019 at 13:43, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto: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:
>
>         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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Zhi Li

3:39 p.m.

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Attached please find the recon-all.log file.

Greve, Douglas N.,Ph.D.

4:08 p.m.

The log file indicates that everything finished successfully. The m3z.inv files are no longer created. The label files are now called, eg, lh.MT_exvivo.label (they have "exvivo" in them). I don't know why the checker is not working, probably needs to be updated for version 6. I don't think a lot of people use it.

On 2/14/19 3:27 PM, Douglas N. Greve wrote:

...

can you send the recon-all.log file?

On 2/14/19 2:55 PM, Zhi Li wrote:

...
External Email - Use Caution

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 mailto: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:     >     >         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     >     >     > _______________________________________________     > Freesurfer mailing list     > Freesurfer@nmr.mgh.harvard.edu     mailto:Freesurfer@nmr.mgh.harvard.edu     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Zhi Li

4:39 p.m.

External Email - Use Caution

I see. Thank you very much.

Best wishes,

Lizhi

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Greve, Douglas N.,Ph.D.
Zhi Li