External Email - Use Caution

Hello M.Douglas,

I’m running the following command: mris_preproc --fsgd FSGD2.fsgd --target fsaverage --hemi lh --meas thickness --out lh.uci_nuci.thikness.00.mgh. Please find attached the log file.

Thank you,

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, August 1, 2023 3:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

External Email - Use Caution That should be enough RAM. What is your command line? Can you send the log file? On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:

External Email - Use Caution Hello FreeSurfer Developers,

I'm conducting the Surface Based Group Analysis explained on the tutoriel (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1GUHd6jcb3HNo2JW2cNzXKQkjoZQAxxwGoJGG2RzAiDcvIH...https://secure-web.cisco.com/1_YynvwS-dkAnt9HfkAib_JfSy9UZxarfHbzK2t54zb7qCQJxUZZt_Vc0ZIEwqIkD7F27OVUNpLeyNZde-aYgOenPT2_ckqjlYPJrCvQk1NftmX9tjie43cnqsBx4LdigIwZDM-b4v8G_ni6Ejmxmt5RrR5FvxVRnilvDjf241utdgvvHDoBVhnmkoaKzRHeBB_hDZqH0hV_cWvaAaHUtdkqONm6sm-wQzdoTTjg5gjgl6LoFmUCN0VW3p1RPOneDtlJhlP40jjialruPa8d6ByiaS7LGnKxKzxk8PWDLZwBXMiOa1ROzLXIKyVPcBy17YNLC1ex_wY2_4xHhz2cm3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0) but I keep getting the error: "Cannot allocate memory" while running the mris_preproc command.

I'm using the data of 355 subjects stored on an external hard drive, and a pc of 23G RAM, but it stops at the 334 subject. I've already tried with a windows and mac of 16G RAM and got the error, so moved to the other one but still getting the same issue. Does anyone have any thoughts on how to trouble-shoot this? or any other alternative solution to run the mris_preproc on all the subjects?

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platforme: Debian 3.16.7

Thank you for your help, -- Wassima MANSSOUR Master Student at INSEA Rabat M2SI - Information Systems & Intelligent Systems IMRB intern-France wmanssour@insea.ac.mamailto:wmanssour@insea.ac.ma wassima.manssour@u-pec.frmailto:wassima.manssour@u-pec.fr

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External Email - Use Caution

Hello M.Yujing,

I’m using the HCP-A cohort (Human Connectome Project – Aging), where the structural MRIs were preprocessed. So, I’m working directly with the FreeSurfer outputs provided. Is it possible that the lh.sphere.reg of this subject is corrupted?

Thank you,

Wassima

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Tuesday, August 1, 2023 10:14 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

External Email - Use Caution This is the error from log:

Reading source surface reg /media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg error: Cannot allocate memory error: TAGskip: tag=116798, failed to calloc 116799 bytes!

The TAG number looks wrong. I’m wondering how you created /media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of MANSSOUR Wassima Sent: Tuesday, August 1, 2023 2:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

External Email - Use Caution Hello M.Douglas,

I’m running the following command: mris_preproc --fsgd FSGD2.fsgd --target fsaverage --hemi lh --meas thickness --out lh.uci_nuci.thikness.00.mgh. Please find attached the log file.

Thank you,

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Tuesday, August 1, 2023 3:52 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

External Email - Use Caution That should be enough RAM. What is your command line? Can you send the log file? On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:

External Email - Use Caution Hello FreeSurfer Developers,

I'm conducting the Surface Based Group Analysis explained on the tutoriel (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1knY1Q4at5jib_1NgTnoMZw4eU0hXHRp-fVAJscsHC-I5Rv...https://secure-web.cisco.com/1_YynvwS-dkAnt9HfkAib_JfSy9UZxarfHbzK2t54zb7qCQJxUZZt_Vc0ZIEwqIkD7F27OVUNpLeyNZde-aYgOenPT2_ckqjlYPJrCvQk1NftmX9tjie43cnqsBx4LdigIwZDM-b4v8G_ni6Ejmxmt5RrR5FvxVRnilvDjf241utdgvvHDoBVhnmkoaKzRHeBB_hDZqH0hV_cWvaAaHUtdkqONm6sm-wQzdoTTjg5gjgl6LoFmUCN0VW3p1RPOneDtlJhlP40jjialruPa8d6ByiaS7LGnKxKzxk8PWDLZwBXMiOa1ROzLXIKyVPcBy17YNLC1ex_wY2_4xHhz2cm3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0) but I keep getting the error: "Cannot allocate memory" while running the mris_preproc command.

I'm using the data of 355 subjects stored on an external hard drive, and a pc of 23G RAM, but it stops at the 334 subject. I've already tried with a windows and mac of 16G RAM and got the error, so moved to the other one but still getting the same issue. Does anyone have any thoughts on how to trouble-shoot this? or any other alternative solution to run the mris_preproc on all the subjects?

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platforme: Debian 3.16.7

Thank you for your help, -- Wassima MANSSOUR Master Student at INSEA Rabat M2SI - Information Systems & Intelligent Systems IMRB intern-France wmanssour@insea.ac.mamailto:wmanssour@insea.ac.ma wassima.manssour@u-pec.frmailto:wassima.manssour@u-pec.fr

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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/196PDYB-5KILx6gfZoR7IAQCSTrro-SP66zwJAhJ4B8oHe0...https://secure-web.cisco.com/1XWcS2l5SicrnDgN4gbTQZt1Nd_cVEWf0etLF5oIpmmmKJs9gwOJvEqy1EbB2fYqaB_TSaMqF-yvzSuh7OGdmU9slvknwXY5PA3sx0ke-37UuFEUPfd75knhtpdzf324gWx7BrDZ711CANLz_duLhFUfVITkflAX9O2Rxd7JcdS2Gk5Le-koV7gjM6kt8ux9WnYzXh7nh0wk8nbIFeeHC9zzXLAAtaA5ThMo8-FltWXsHSj0RRqEtAeJYLDH8lXQsIPHgKs7NpLE_kyAXSe3DqA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

External Email - Use Caution

You are right! same error: error: Cannot allocate memory error: TAGskip: tag=116798, failed to calloc 116799 bytes!

while it works for another subject! Thank you, I'll re-download it and retry the commands.

Wassima ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDU Sent: Tuesday, August 1, 2023 10:15 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

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It looks like it is corrupted.

Can you try ‘mris_info /media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg’? I think it probably will fail the same way.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of MANSSOUR Wassima Sent: Tuesday, August 1, 2023 4:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

External Email - Use Caution

Hello M.Yujing,

I’m using the HCP-A cohort (Human Connectome Project – Aging), where the structural MRIs were preprocessed. So, I’m working directly with the FreeSurfer outputs provided.

Is it possible that the lh.sphere.reg of this subject is corrupted?

Thank you,

Wassima

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Tuesday, August 1, 2023 10:14 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

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This is the error from log:

Reading source surface reg /media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg

error: Cannot allocate memory

error: TAGskip: tag=116798, failed to calloc 116799 bytes!

The TAG number looks wrong. I’m wondering how you created /media/sf_T1/freesurfer_results/HCA9679715_V1_MR/surf/lh.sphere.reg?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of MANSSOUR Wassima Sent: Tuesday, August 1, 2023 2:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

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Hello M.Douglas,

I’m running the following command: mris_preproc --fsgd FSGD2.fsgd --target fsaverage --hemi lh --meas thickness --out lh.uci_nuci.thikness.00.mgh.

Please find attached the log file.

Thank you,

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Tuesday, August 1, 2023 3:52 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc error: cannot allocate memory

External Email - Use Caution

That should be enough RAM. What is your command line? Can you send the log file?

On 8/1/2023 7:52 AM, MANSSOUR Wassima wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I'm conducting the Surface Based Group Analysis explained on the tutoriel (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1hOHo9dwuADs5lxHpMgQrwfxmQTVEAHHditOqIlDKkvBzI0...https://secure-web.cisco.com/1_YynvwS-dkAnt9HfkAib_JfSy9UZxarfHbzK2t54zb7qCQJxUZZt_Vc0ZIEwqIkD7F27OVUNpLeyNZde-aYgOenPT2_ckqjlYPJrCvQk1NftmX9tjie43cnqsBx4LdigIwZDM-b4v8G_ni6Ejmxmt5RrR5FvxVRnilvDjf241utdgvvHDoBVhnmkoaKzRHeBB_hDZqH0hV_cWvaAaHUtdkqONm6sm-wQzdoTTjg5gjgl6LoFmUCN0VW3p1RPOneDtlJhlP40jjialruPa8d6ByiaS7LGnKxKzxk8PWDLZwBXMiOa1ROzLXIKyVPcBy17YNLC1ex_wY2_4xHhz2cm3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0)

but I keep getting the error: "Cannot allocate memory" while running the mris_preproc command.

I'm using the data of 355 subjects stored on an external hard drive, and a pc of 23G RAM, but it stops at the 334 subject.

I've already tried with a windows and mac of 16G RAM and got the error, so moved to the other one but still getting the same issue.

Does anyone have any thoughts on how to trouble-shoot this? or any other alternative solution to run the mris_preproc on all the subjects?

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0

Platforme: Debian 3.16.7

Thank you for your help,

--

Wassima MANSSOUR

Master Student at INSEA Rabat

M2SI - Information Systems & Intelligent Systems

IMRB intern-France

wmanssour@insea.ac.mamailto:wmanssour@insea.ac.ma

wassima.manssour@u-pec.frmailto:wassima.manssour@u-pec.fr

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