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| | Dear freesurfer experts, I am trying to run recon-all with -hippocampal-subfields-T1 flag to get hippocampal subfield information. I tried many times but always finish with error. The MRI data is obtained from GE750 MRI machine. The resolution is 1mm*1mm*1mm.
below is the commands I used to run freesurfer and attached is the recon-all log file.
recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all I am not sure if there are something wrong with my inputs.
Thank you all all the best Shize
--
Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13@fudan.edu.cn
| | | |
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Hi Shize, Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me … 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 姜时泽 jiangshize1990@163.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 23 August 2018 at 15:10 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Dear freesurfer experts, I am trying to run recon-all with -hippocampal-subfields-T1 flag to get hippocampal subfield information. I tried many times but always finish with error. The MRI data is obtained from GE750 MRI machine. The resolution is 1mm*1mm*1mm.
below is the commands I used to run freesurfer and attached is the recon-all log file.
recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all I am not sure if there are something wrong with my inputs.
Thank you all all the best Shize
--
Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13@fudan.edu.cnmailto:sjiang13@fudan.edu.cn
[mage removed by sender.]
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Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you
Shize
在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
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Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio
External Email - Use Caution
Thanks! Can you please send us the log of the hippocampal subfield segmentation? It should be in the same directory as the recon-all log.
Cheers,
/E
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of 姜时泽 jiangshize1990@163.com Sent: Thursday, August 23, 2018 5:08:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you Shize
在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
External Email - Use Caution
Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 23 August 2018 at 15:10 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Dear freesurfer experts,
I am trying to run recon-all with -hippocampal-subfields-T1 flag to get hippocampal subfield information. I tried many times but always finish with error. The MRI data is obtained from GE750 MRI machine. The resolution is 1mm*1mm*1mm.
below is the commands I used to run freesurfer and attached is the recon-all log file.
recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all
I am not sure if there are something wrong with my inputs.
Thank you all
all the best
Shize
--
Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13@fudan.edu.cnmailto:sjiang13@fudan.edu.cn
[mage removed by sender.]
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Hi Juan Thank you for your kindly help. Attached is the log file with error. I am not sure if this is the file for hippocampus subfield segmentation.
Thank you very much
Shize
在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
External Email - Use Caution
Thanks! Can you please send us the log of the hippocampal subfield segmentation? It should be in the same directory as the recon-all log.
Cheers,
/E
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
From:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of 姜时泽 jiangshize1990@163.com Sent: Thursday, August 23, 2018 5:08:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you
Shize
在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
External Email - Use Caution
Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio
External Email - Use Caution
I am really confused. There are no errors in the subfield module in that log. Can you please send me the file hippocampal-subfields-T1.log, which should be found in the scripts directory (inside the subject’s directory)? 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 姜时泽 jiangshize1990@163.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 23 August 2018 at 23:02 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Juan Thank you for your kindly help. Attached is the log file with error. I am not sure if this is the file for hippocampus subfield segmentation. Thank you very much Shize
在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
External Email - Use Caution
Thanks! Can you please send us the log of the hippocampal subfield segmentation? It should be in the same directory as the recon-all log.
Cheers,
/E
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
________________________________ 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 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Sent: Thursday, August 23, 2018 5:08:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you Shize
在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> 写道：
External Email - Use Caution
Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 23 August 2018 at 15:10 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Dear freesurfer experts,
I am trying to run recon-all with -hippocampal-subfields-T1 flag to get hippocampal subfield information. I tried many times but always finish with error. The MRI data is obtained from GE750 MRI machine. The resolution is 1mm*1mm*1mm.
below is the commands I used to run freesurfer and attached is the recon-all log file.
recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all
I am not sure if there are something wrong with my inputs.
Thank you all
all the best
Shize
--
Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13@fudan.edu.cnmailto:sjiang13@fudan.edu.cn
[age removed by sender.]
External Email - Use Caution
Hi Eugenio I did not find the log file you mentioned. Attached is all log file within script directory. Would you please help me to figure out what was wrong? Thank you so much Best wishes
Shize
在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
External Email - Use Caution
I am really confused. There are no errors in the subfield module in that log.
Can you please send me the file hippocampal-subfields-T1.log, which should be found in the scripts directory (inside the subject’s directory)?
Cheers,
/Eugenio
External Email - Use Caution
The subfield part never started. Recon-all died earlier. Andrew: any ideas?
-- 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 姜时泽 jiangshize1990@163.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 24 August 2018 at 15:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Eugenio I did not find the log file you mentioned. Attached is all log file within script directory. Would you please help me to figure out what was wrong? Thank you so much Best wishes Shize
在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
External Email - Use Caution I am really confused. There are no errors in the subfield module in that log. Can you please send me the file hippocampal-subfields-T1.log, which should be found in the scripts directory (inside the subject’s directory)? 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 23 August 2018 at 23:02 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Juan Thank you for your kindly help. Attached is the log file with error. I am not sure if this is the file for hippocampus subfield segmentation. Thank you very much Shize
在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> 写道：
External Email - Use Caution
Thanks! Can you please send us the log of the hippocampal subfield segmentation? It should be in the same directory as the recon-all log.
Cheers,
/E
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
________________________________ 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 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Sent: Thursday, August 23, 2018 5:08:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you Shize
在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> 写道：
External Email - Use Caution
Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 23 August 2018 at 15:10 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Dear freesurfer experts,
I am trying to run recon-all with -hippocampal-subfields-T1 flag to get hippocampal subfield information. I tried many times but always finish with error. The MRI data is obtained from GE750 MRI machine. The resolution is 1mm*1mm*1mm.
below is the commands I used to run freesurfer and attached is the recon-all log file.
recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all
I am not sure if there are something wrong with my inputs.
Thank you all
all the best
Shize
--
Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13@fudan.edu.cnmailto:sjiang13@fudan.edu.cn
[ge removed by sender.]
I’m not completely sure, but I think I have a general idea. The error log claims that mris_anatomical_stats is failing, but the output seems to indicate it finishes successfully. I’m guessing one of the initial subfield steps is actually erroring out because in the v6 recon-all, mris_anatomical_stats is called right before subfield processing, and since the “cmd” variable is never set and none of the errors are redirected, it’s impossible to tell what the issue is by looking at logs.
To see the errors, you’ll have to look back on the real output originally sent to stdout. If you no longer have access to this, you’ll unfortunately have to rerun recon-all locally, where you can view the direct output in the terminal. Alternatively, you could rerun recon-all and redirect stdout to a file with something like:
recon-all > log.txt
Hope that helps, Andrew
PS. to potentially save some time, you might want to first check if you have the matlab 2012b runtime stored at ${FREESURFER_HOME}/MCRv80 because this is most likely what the hidden issue is
From: "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk Date: Friday, August 24, 2018 at 7:20 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Cc: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution The subfield part never started. Recon-all died earlier. Andrew: any ideas?
-- 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 姜时泽 jiangshize1990@163.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 24 August 2018 at 15:14 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Eugenio I did not find the log file you mentioned. Attached is all log file within script directory. Would you please help me to figure out what was wrong? Thank you so much Best wishes Shize
在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk 写道：
External Email - Use Caution I am really confused. There are no errors in the subfield module in that log. Can you please send me the file hippocampal-subfields-T1.log, which should be found in the scripts directory (inside the subject’s directory)? 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 23 August 2018 at 23:02 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Juan Thank you for your kindly help. Attached is the log file with error. I am not sure if this is the file for hippocampus subfield segmentation. Thank you very much Shize
在 2018-08-24 05:08:35，"Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> 写道：
External Email - Use Caution
Thanks! Can you please send us the log of the hippocampal subfield segmentation? It should be in the same directory as the recon-all log.
Cheers,
/E
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
________________________________ 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 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Sent: Thursday, August 23, 2018 5:08:51 PM To: Freesurfer support list Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you Shize
在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> 写道：
External Email - Use Caution
Hi Shize,
Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me …
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 姜时泽 <jiangshize1990@163.commailto:jiangshize1990@163.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 23 August 2018 at 15:10 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Dear freesurfer experts,
I am trying to run recon-all with -hippocampal-subfields-T1 flag to get hippocampal subfield information. I tried many times but always finish with error. The MRI data is obtained from GE750 MRI machine. The resolution is 1mm*1mm*1mm.
below is the commands I used to run freesurfer and attached is the recon-all log file.
recon-all SubJ01_ReoT1.nii -s SubJ01_ReoT13THip -hippocampal-subfields-T1 -brainstem-structures -3T -qcache -all
I am not sure if there are something wrong with my inputs.
Thank you all
all the best
Shize
--
Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13@fudan.edu.cnmailto:sjiang13@fudan.edu.cn
[ge removed by sender.]
freesurfer@nmr.mgh.harvard.edu
-
Hoopes, Andrew -
Iglesias Gonzalez, Eugenio -
姜时泽