External Email - Use Caution
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
External Email - Use Caution 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 -------------- 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
External Email - Use Caution
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
External Email - Use Caution 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.comhttp://www.jeiglesias.com/
From: <freesurfer-bounceshttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> on behalf of 墨初 <530337973https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at qq.comhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Reply-To: Freesurfer support list <freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Date: Tuesday, 17 July 2018 at 13:40
To: freesurfer <freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Subject: [Freesurfer] segmentHA_T2.sh
External Email - Use Caution
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
--------------
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution 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
External Email - Use Caution 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.comhttp://www.jeiglesias.com/
From: <freesurfer-bounceshttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> on behalf of 墨初 <530337973https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at qq.comhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Reply-To: Freesurfer support list <freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Date: Tuesday, 17 July 2018 at 13:40
To: freesurfer <freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Subject: [Freesurfer] segmentHA_T2.sh
External Email - Use Caution
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
--------------
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
Thanks! I am fairly confident it's a memory issue, then. Do you have access to a machine with more RAM you can test the code on?
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: Thursday, July 19, 2018 5:27:46 AM To: Freesurfer support list Subject: [Freesurfer] Re： Re： Re：segmentHA_T2.sh
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution 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
External Email - Use Caution 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.comhttp://www.jeiglesias.com/
From: <freesurfer-bounceshttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> on behalf of 墨初 <530337973https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at qq.comhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Reply-To: Freesurfer support list <freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Date: Tuesday, 17 July 2018 at 13:40
To: freesurfer <freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer at nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Subject: [Freesurfer] segmentHA_T2.sh
External Email - Use Caution
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
--------------
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
External Email - Use Caution
Thanks,
I am very sorry for the late reply. I didn't have a machine with more RAM at present,but i ran the code on another machine(mac mini,4G or 8G LPDDR3 SDRAM ,500GB) several month ago. it ran well.so i didn't certain it. I will try to test the code on a machine with more RAM if I get the opportunity. Thanks for your help . 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19日(星期四) 下午3:54 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;"Freesurfersupport list"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer]Re： Re： Re：segmentHA_T2.sh
External Email - Use Caution
Thanks! I am fairly confident it's a memory issue, then. Do you have access to a machine with more RAM you can test the code on?
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: Thursday, July 19, 2018 5:27:46 AM To: Freesurfer support list Subject: [Freesurfer] Re： Re： Re：segmentHA_T2.sh
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
External Email - Use Caution
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
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Eugenio -
墨初