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) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wei Shao wshao@research.baycrest.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, April 29, 2021 at 22:39 To: Freesurfer support list 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 <wshao@research.baycrest.orgmailto:wshao@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

Yeah that’s what we do at the Martinos cluster ;-) I’m glad it’s working!

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wei Shao wshao@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. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@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) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1tjk3OL0B6Drsa3xCXMNVuI8sfeKEW4_XP4tWvrd_ajd5F67eazolqhGpHBgeo1L5gH3VYBePfywpla8y2ELEjhHj1D_-3_bryJu2GGFeyDr4m-hTdINqzbyWpmow9_PjNYF_DqMZlL3XYdJBbhnPCzF1vNFprQS0wyIi3mkq--Hd5NeqhDQeCl6ARiRfGOVFCxYDP9144ghi_gvC_eFPX_NN0eEYiK4ddz8MNB3EFMEj7YGCYWJC3Zh9V7kKMIVVAwuETkeZx9JyiEy1lCxeXg/http%3A%2F%2Fwww.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wei Shao <wshao@research.baycrest.orgmailto:wshao@research.baycrest.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, April 29, 2021 at 22:39 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 <wshao@research.baycrest.orgmailto:wshao@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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