Yeah that’s what we do at the Martinos cluster ;-)
I’m glad it’s working!
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wei Shao
<ws...@research.baycrest.org>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, April 30, 2021 at 19:19
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Out of memory from longitudinal segmentation of
hippocampus
External Email - Use Caution
Hi, E
Thanks for your reply, I used one core and its associated RAM from the
server,(I guess is not very much) but I have solved it by assigning more RAM
memory.
Best,
Wei
On Fri, Apr 30, 2021 at 9:35 AM Iglesias Gonzalez, Juan E.
<jiglesiasgonza...@mgh.harvard.edu<mailto:jiglesiasgonza...@mgh.harvard.edu>>
wrote:
Dear Wei,
Sorry for missing your message (it happens sometimes…).
The longitudinal subfield module is very RAM memory hungry.
How much RAM memory do you have (not disk space, these are different things).
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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From:
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Wei Shao
<ws...@research.baycrest.org<mailto:ws...@research.baycrest.org>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, April 29, 2021 at 22:39
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Out of memory from longitudinal segmentation of
hippocampus
External Email - Use Caution
Hello, Dear Freesufer experts
I just thought of sending a friendly reminder -
I am wondering if you had the time to go over my question?
Best regards,
Wei
On Sat, Apr 24, 2021 at 2:26 PM Wei Shao
<ws...@research.baycrest.org<mailto:ws...@research.baycrest.org>> wrote:
Hello, Dear FreeSurfer expert.
I was tried to use longitudinal segmentation of T1 scans for the longitudinal
analysis. but there is a problem
making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Error using permute
Out of memory. Type HELP MEMORY for your options.
Error in myMRIread>myMRIread_aux (line 99)
Error in myMRIread (line 63)
Error in SegmentSubfieldsT1Longitudinal (line 904)
MATLAB:nomem
@#@FSTIME 2021:04:24:13:57:21 run_SegmentSubfieldsT1Longitudinal.sh N 17 e
249.25 S 49.95 U 759.76 P 324% M 1532492 F 249 R 4682496 W 0 c 134624 w 550491
I 3940880 O 1217536 L 1.24 1.04 1.58
@#@FSLOADPOST 2021:04:24:14:01:30 run_SegmentSubfieldsT1Longitudinal.sh N 17
4.04 3.43 2.47
Linux gra-login1 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020
x86_64 GNU/Linux
longitudinal subfields exited with ERRORS at Sat Apr 24 14:01:31 EDT 2021
For more details, see the log file
/home/weishao/long_BAY12019/scripts/long-hippocampal-subfields-T1.log
I have checked the space:
Description Space # of files
/home (user weishao) 44G/53G
147k/500k
Could you tell me what I should do? Thanks
Best,
Cheer
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