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I tried to run"segmentHA_T2.sh subject001 T2.nii T2 0" and "segmentHA_T1.sh subject003", it's well done! When run

Thanks,

Fiona

------------------ 原始邮件 ------------------

发件人: "Iglesias Gonzalez, Eugenio"<e.iglesias@ucl.ac.uk>;

发送时间: 2018年7月18日(星期三) 晚上8:35

收件人: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;"Freesurfersupport list"<freesurfer@nmr.mgh.harvard.edu>;

主题: Re: [Freesurfer] Re： Re：segmentHA_T2.sh

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Thanks!

Do you have the same problem if you use the T2 alone? For instance

segmentHA_T2.sh subject001 T2.nii T2 0

Sent from my phone, please excuse brevity and typos

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 墨初 <530337973@qq.com>
Sent: Wednesday, July 18, 2018 1:21:25 PM
To: Freesurfer support list
Subject: [Freesurfer] Re： Re：segmentHA_T2.sh

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Dear Eugenio,

I tried 3 subjects ,it dies at the same step ,and it stops there all the time even 3 days. No error reported here.

Thanks ,

Fiona Ding.

------------------ 原始邮件 ------------------

发件人: "Iglesias Gonzalez, Eugenio"<e.iglesias@ucl.ac.uk>;

发送时间: 2018年7月18日(星期三) 晚上7:29

收件人: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>;

主题: Re: [Freesurfer] Re：segmentHA_T2.sh

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Thanks, Fiona.

Is the error reproducible? Does it always die at the same step? Do you get the same problem with other subjects?

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 墨初 <530337973@qq.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 18 July 2018 at 10:15
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re：segmentHA_T2.sh

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hello，

I think RAM is enough。my computer is imac pro.There is 16G DDDR3. This process takes up about 1-2G. The total RAM occupied is 5G. Thanks Fiona Ding.

---------------- External Email - Use Caution Weird! Maybe you ran out of RAM memory?

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces

at nmr.mgh.harvard.edu>

on behalf of 墨初 <530337973

at qq.com>

Reply-To: Freesurfer support list <freesurfer

at nmr.mgh.harvard.edu>

Date: Tuesday, 17 July 2018 at 13:40

To: freesurfer <freesurfer

at nmr.mgh.harvard.edu>

Subject: [Freesurfer] segmentHA_T2.sh

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Dear freesurfer experts,

when i run the command“segmentHA_T2.sh subject001 T2.nii T2 1” ,it runs as following:

--------------

Making Left-Thalamus-Proper map to reduced label 10

--------------

Making Left-choroid-plexus map to reduced label 11

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Making Left-VentralDC map to reduced label 12

--------------

Making Left-Accumbens-area map to reduced label 13

--------------

Making Unknown map to reduced label 14

Computing hyperparameters for estimation of Gaussians parameters

znzreadInt: znzread failed

No such file or directory

Estimating typical intensities of molecular layer and alveus

numberOfLabels: 2

Rasterizing mesh...here: 2

here2: 2

done

Smoothing mesh collection with kernel size 1.500000 ...Smoothing class: 0

Smoothing class: 1

Smoothing class: 2

Smoothing class: 3

Smoothing class: 4

Smoothing class: 5

Smoothing class: 6

Smoothing class: 7

Smoothing class: 8

Smoothing class: 9

Smoothing class: 10

Smoothing class: 11

Smoothing class: 12

Smoothing class: 13

done

numberOfImages = 2

Image: 0

Image: 2

Iteration 1 of 7

1 0.00035804

2 0.089592

fianally,it stop here and can't run anymore,no error reported。I didn't know what‘s wrong？

What can i do？

Thanks very much

Fiona Ding