Hi Bruce! 

 

thank you for your kind reply.

 

I will change the total memory like this and recon-all again.

 

             total       used       free     shared    buffers     cached

Mem:      17656648    3976936   13679712       1316       9660    3472344

-/+ buffers/cache:     494932   17161716

Swap:      3145724          0    3145724

 

But I'm wondering is this not a problem? 

 

recon-all.error say

root@620b39bc3276:/opt/freesurfer/subjects/subject1/scripts# cat recon-all.error 

PWD /opt/freesurfer/subjects/subject1/mri

CMD mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz

​ 

Kyul

 

-----Original Message-----
From: "Bruce Fischl"<fischl@nmr.mgh.harvard.edu>
To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;
Cc:
Sent: 2018-07-15 (일) 01:10:28
Subject: Re: [Freesurfer] recon-all error: I think mri_ca_label problem...
 

Hi Kyul

I'm pretty sure you ran out of memory. We typically recommend 8G of RAM:

https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements

I you look in your recon-all.log file it shows total and free memory:


             total       used       free     shared    buffers     cached
Mem:       2027764    1203512     824252       3716     148744     502072
-/+ buffers/cache:     552696    1475068
Swap:      1048572     714068     334504

(this is the output of the unix command /usr/bin/free)

You have only 2G in the machine, but more than half of it is in use when
recon-all starts executing. You might be able to get away with 2G if most
of it was free, but I don't think things will run in 800MB

cheers
Bruce


On Sat, 14 Jul 2018, 김결 wrote:

>
>         External Email - Use Caution        
>
>
>  
>
> Hello FreeSurfer Developers,
>
>  
>
> I'm attempting to recon-all function (input file is sample-001.nii.gz), but for some of my subjects
> I get the following error when I run the recon-all command:
>
>  
>
> I've searched the list and no similar errors have been reported. Does anyone have any thoughts on
> how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 
>
>  
>
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
>
> 2) Platform: Docker freesurfer/freesurfer tag 6.0 (maybe officialized 
>
> 3) recon-all.log: see attached
>
> 4) recon-all.error.log see attached
>
> 5) recon-all-status see attached
>
>  
>
> please help me...
>
>  
>
> Kyul
>
> [?img=0rbrKAFq1HJ4Mq30hAnmaxElK6i0KrK%2FK6twKxgrp4kvFo2ZFAMrKov9FvIo%2BrkSKxb5W4d5W4C5bX0q%2BzkR74F
> TWx%2FspNi0pBF9b4p0bvI5WBU5W6%2Bc74CCbNpCb4t5p639.gif]
>

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