freesurfer recon-all crash

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Pavan Chaggar

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Jun 16, 2021, 5:24:30 AM6/16/21

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Hello,

I'm running t1-freesurfer on ~70 subjects. The process crashed but unfortunately I was unable to see the error message because I was running it in a screen session and the terminal output was cut off. I'm trying to resume the pipeline to see the error. The first error I get is:

```

[10:13:29] The t1-freesurfer pipeline finished with errors.

CAPS outputs were not found for 64 image(s):

sub-ADNI116S6100 | ses-M00, ses-M24, ses-M12

sub-ADNI116S6133 | ses-M12, ses-M24, ses-M00

sub-ADNI127S1427 | ses-M120, ses-M132, ses-M144

sub-ADNI127S2234 | ses-M108, ses-M96, ses-M84

sub-ADNI127S4197 | ses-M84, ses-M72

sub-ADNI127S4198 | ses-M84, ses-M72

sub-ADNI127S4301 | ses-M72, ses-M60

sub-ADNI127S5185 | ses-M72, ses-M48, ses-M60

sub-ADNI127S5200 | ses-M60, ses-M72, ses-M48

sub-ADNI127S5266 | ses-M48, ses-M60, ses-M72

sub-ADNI128S2002 | ses-M108, ses-M96

sub-ADNI128S4742 | ses-M72, ses-M84

sub-ADNI129S2332 | ses-M84, ses-M96, ses-M72

sub-ADNI129S4422 | ses-M72, ses-M60

sub-ADNI135S4356 | ses-M72, ses-M84, ses-M96

sub-ADNI135S4489 | ses-M84, ses-M60, ses-M72

sub-ADNI135S4723 | ses-M72, ses-M84, ses-M96, ses-M60

sub-ADNI135S6104 | ses-M24, ses-M12, ses-M00

sub-ADNI135S6110 | ses-M12, ses-M24, ses-M36, ses-M00

sub-ADNI137S4862 | ses-M60, ses-M72, ses-M84

sub-ADNI141S6061 | ses-M00, ses-M12, ses-M24

sub-ADNI141S6116 | ses-M24, ses-M00

sub-ADNI168S6142 | ses-M12, ses-M24, ses-M00

```

When I open the crash files the error shown is:

```

ERROR: it appears that recon-all is already running

for sub-ADNI127S2234_ses-M84 based on the presence of /scratch/oxmbm-shared/Image-Data/ADNI/sMRI-Tau/t1-freesurfer/ReconAll/sub-ADNI127S2234_ses-M84/sub-ADNI127S2234_ses-M84/scripts/IsRunning.lh+rh. 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 /scratch/oxmbm-shared/Image-Data/ADNI/sMRI-Tau/t1-freesurfer/ReconAll/sub-ADNI127S2234_ses-M84/sub-ADNI127S2234_ses-M84/scripts/IsRunning.lh+rh

and re-run. Or you can add -no-isrunning to the recon-all

command-line. The contents of this file are:

```

There aren't any recon-all processes running. How can I convey this information through clinica to say that there are no recon-all processes running for any subjects?

Thanks,

Pavan

Omar Rifai

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Jul 6, 2021, 5:35:45 AM7/6/21

to Clinica

Hello Pavan,

You should be able to re-run the pipeline by removing the temporary file:

/scratch/oxmbm-shared/Image-Data/ADNI/sMRI-Tau/t1-freesurfer/ReconAll/sub-ADNI127S2234_ses-M84/sub-ADNI127S2234_ses-M84/scripts/IsRunning.lh+rh