External Email - Use Caution
Dear Bruce Fischl, I am very sorry that I have not reply to you last week. Our data has been running for a few weeks, but the computer did not react. There is a log file in the attachment. We want to ask that could you help us run the data? We will send you a set of data firstly(We still have two sets of data). If you can help us run our high resolution data, we will be very grateful. And can we write your name in the acknowledgments section? Our tutor is now at Boston Children's Hospital (BCH). If possible, she would like to consult you in person.
The download link is: https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=d... https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=d...
Looking forward to your reply. Thanks in advance
yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; 发送时间: 2018年11月7日(星期三) 凌晨2:42 收件人: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer] ?????? Recon-all run error
does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix.
On Tue, 6 Nov 2018, 1013364183 wrote:
External Email - Use CautionDear Bruce, I found the error location in the recon-all.log folder. Here is the place where it went wrong??I don't think it's the reason for insufficient memory.. ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 version and set the expert file, this error will occur.Do I need to step through the instructions to see the problem? How should this error be solved?
Thanks in advance
yours yujunjie
------------------ ???????? ------------------ ??????: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; ????????: 2018??11??6??(??????) ????9:40 ??????: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; ????: Re: [Freesurfer] Recon-all run error
that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it works? Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file
cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote:
External Email - Use CautionDear FS, When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the
mri_convert
command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) mri_convert.bin "$@" ERROR: converting to minc We want to know if our high resolution image is too large for freesurfer to handle, or our
computer
memory (64GB running memory) is limited.
Thanks a lot in advance! yours sincerely, yu junjie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It looks like you might have a very big defect. Probably there is a bit of skull or cerebellum still attached. Follow the tutorial for checking for and fixing defects.
On 11/14/2018 02:59 AM, 1013364183 wrote:
External Email - Use Caution
Dear Bruce Fischl, I am very sorry that I have not reply to you last week. Our data has been running for a few weeks, but the computer did not react. There is a log file in the attachment. We want to ask that could you help us run the data? We will send you a set of data firstly(We still have two sets of data). If you can help us run our high resolution data, we will be very grateful. And can we write your name in the acknowledgments section? Our tutor is now at Boston Children's Hospital (BCH). If possible, she would like to consult you in person. The download link is: https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=d... https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=d...
Looking forward to your reply. Thanks in advance
yours yujunjie ------------------ 原始邮件 ------------------ *发件人:* "Bruce Fischl"fischl@nmr.mgh.harvard.edu; *发送时间:* 2018年11月7日(星期三) 凌晨2:42 *收件人:* "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; *主题:* Re: [Freesurfer] ?????? Recon-all run error
does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix.
On Tue, 6 Nov 2018, 1013364183 wrote:
External Email - Use Caution
Dear Bruce, I found the error location in the recon-all.log folder. Here is
the place where it went wrong??I
don't think it's the reason for insufficient memory.. ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz %
4 == 0' failed.''
This data is ok when we run with versions prior to freesurfer 6.0.
But after we run the 6.0
version and set the expert file, this error will occur.Do I need to
step through the instructions to
see the problem? How should this error be solved?
Thanks in advance
yours yujunjie
------------------ ???????? ------------------ ??????: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; ????????: 2018??11??6??(??????) ????9:40 ??????: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; ????: Re: [Freesurfer] Recon-all run error
that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it
works?
Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file
cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote:
External Email - Use Caution
Dear FS, When we run ??recon-all?? with a 5GB high-resolution image, core
dumped appears when the
mri_convert
command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3:
29235 Aborted (core dumped)
mri_convert.bin "$@" ERROR: converting to minc We want to know if our high resolution image is too large for
freesurfer to handle, or our
computer
memory (64GB running memory) is limited.
Thanks a lot in advance! yours sincerely, yu junjie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Greve, Thank you very much for your reply.Where is the tutorial for checking for and fixing defects? Is it the link below? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFixV6.0
yours yujunjie
------------------ 原始邮件 ------------------ 发件人: "Greve, Douglas N.,Ph.D."DGREVE@mgh.harvard.edu; 发送时间: 2018年11月15日(星期四) 凌晨5:12 收件人: "freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu;
主题: Re: [Freesurfer]回复： ?????? Recon-all run error
It looks like you might have a very big defect. Probably there is a bit of skull or cerebellum still attached. Follow the tutorial for checking for and fixing defects.
On 11/14/2018 02:59 AM, 1013364183 wrote:
External Email - Use CautionDear Bruce Fischl, I am very sorry that I have not reply to you last week. Our data has been running for a few weeks, but the computer did not react. There is a log file in the attachment. We want to ask that could you help us run the data? We will send you a set of data firstly(We still have two sets of data). If you can help us run our high resolution data, we will be very grateful. And can we write your name in the acknowledgments section? Our tutor is now at Boston Children's Hospital (BCH). If possible, she would like to consult you in person. The download link is: https://drive.google.com/file/d/1_5tYKHipNOTFe96p4BOMc1kbNPK1O93W/view?usp=d... https://drive.google.com/file/d/12TZ0_J_njiZju9PDyvwxnHIiDe8D5SOA/view?usp=d...
Looking forward to your reply. Thanks in advance
yours yujunjie ------------------ 原始邮件 ------------------ *发件人:* "Bruce Fischl"fischl@nmr.mgh.harvard.edu; *发送时间:* 2018年11月7日(星期三) 凌晨2:42 *收件人:* "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; *主题:* Re: [Freesurfer] ?????? Recon-all run error
does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix.
On Tue, 6 Nov 2018, 1013364183 wrote:
External Email - Use CautionDear Bruce, I found the error location in the recon-all.log folder. Here is
the place where it went wrong??I
don't think it's the reason for insufficient memory.. ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz %
4 == 0' failed.''
This data is ok when we run with versions prior to freesurfer 6.0.
But after we run the 6.0
version and set the expert file, this error will occur.Do I need to
step through the instructions to
see the problem? How should this error be solved?
Thanks in advance
yours yujunjie
------------------ ???????? ------------------ ??????: "Bruce Fischl"fischl@nmr.mgh.harvard.edu; ????????: 2018??11??6??(??????) ????9:40 ??????: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu; ????: Re: [Freesurfer] Recon-all run error
that certainly looks like something is running out of ram. Can you run the command that failed directly on the command line and see if it
works?
Was anything else running on the machine at the time? We do report total and free memory at the start of the recon in the recon-all.log file
cheers Bruce On Tue, 6 Nov 2018, 1013364183 wrote:
External Email - Use CautionDear FS, When we run ??recon-all?? with a 5GB high-resolution image, core
dumped appears when the
mri_convert
command is executed. The specific errors are as follows: /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3:
29235 Aborted (core dumped)
mri_convert.bin "$@" ERROR: converting to minc We want to know if our high resolution image is too large for
freesurfer to handle, or our
computer
memory (64GB running memory) is limited.
Thanks a lot in advance! yours sincerely, yu junjie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
1013364183 -
Greve, Douglas N.,Ph.D.