External Email - Use Caution

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]

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

External Email - Use Caution

Hi Bruce!

You are right! The problem is solved by raising the memory capacity.

Next time someone else asks you to solve the mri_ca_label problem, tell them to increase their machine memory!

thank you very much.

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]

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.