Re: [Freesurfer] 回复: The file absence problem of the recon-all -all output

[Douglas N. Greve]

Use orig.mgz

On 6/27/2024 9:47 PM, Quanjiang Liu wrote:


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  Sorry to bother you again. I want to know that the standard input to 
get the standard lh.seghead and rh.seghead. Is it the T1.mgz or the 
brain.mgz in the mri folder which is one of the output files of 
recon-all -all command.

Best,


*发件人:* freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N. Greve 


*发送时间:* 2024年6月27日 6:35
*收件人:* freesurfer@nmr.mgh.harvard.edu 
*主题:* Re: [Freesurfer] The file absence problem of the recon-all -all 
output



你通常不会收到来自 dgr...@mgh.harvard.edu 
的电子邮件。了解这一点为什么很重要 




that has to be created with a separate process (mri_seghead)

On 6/26/2024 2:11 PM, Quanjiang Liu wrote:


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  Hi, I ran the recon-all -all command successfully. But the 
lh.seghead and rh.seghead didn't appear in my output folder. The 
attachment is the process record. Can you help to solve it?

  Sorry to bother.
Best

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[Freesurfer] 回复: The file absence problem of the recon-all -all output

[Quanjiang Liu]

External Email - Use Caution

  Sorry to bother you again. I want to know that the standard input to get the 
standard lh.seghead and rh.seghead. Is it the T1.mgz or the brain.mgz in the 
mri folder which is one of the output files of recon-all -all command.
Best,


发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N. Greve 

发送时间: 2024年6月27日 6:35
收件人: freesurfer@nmr.mgh.harvard.edu 
主题: Re: [Freesurfer] The file absence problem of the recon-all -all output

你通常不会收到来自 dgr...@mgh.harvard.edu 
的电子邮件。了解这一点为什么很重要
that has to be created with a separate process (mri_seghead)

On 6/26/2024 2:11 PM, Quanjiang Liu wrote:

External Email - Use Caution

  Hi, I ran the recon-all -all command successfully. But the lh.seghead and 
rh.seghead didn't appear in my output folder. The attachment is the process 
record. Can you help to solve it?
  Sorry to bother.
Best



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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] 回复: The file absence problem of the recon-all -all output

[Quanjiang Liu]

External Email - Use Caution

Thank you!

发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N. Greve 

发送时间: 2024年6月27日 6:35
收件人: freesurfer@nmr.mgh.harvard.edu 
主题: Re: [Freesurfer] The file absence problem of the recon-all -all output

你通常不会收到来自 dgr...@mgh.harvard.edu 
的电子邮件。了解这一点为什么很重要
that has to be created with a separate process (mri_seghead)

On 6/26/2024 2:11 PM, Quanjiang Liu wrote:

External Email - Use Caution

  Hi, I ran the recon-all -all command successfully. But the lh.seghead and 
rh.seghead didn't appear in my output folder. The attachment is the process 
record. Can you help to solve it?
  Sorry to bother.
Best



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[Freesurfer] 回复: The file absence problem of the recon-all -all output

[Quanjiang Liu]

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The command used by me is below:

find $input_dir -name "sub-CC1*.nii.gz" | parallel -j $threads recon-all -i {} 
-s {.} -all -qcache


发件人: Quanjiang Liu
发送时间: 2024年6月27日 2:11
收件人: freesurfer@nmr.mgh.harvard.edu 
主题: The file absence problem of the recon-all -all output

  Hi, I ran the recon-all -all command successfully. But the lh.seghead and 
rh.seghead didn't appear in my output folder. The attachment is the process 
record. Can you help to solve it?
  Sorry to bother.
Best
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] 回复: The file absence problem of the recon-all -all output

[Quanjiang Liu]

External Email - Use Caution

[https://res.public.onecdn.static.microsoft/assets/mail/file-icon/png/generic_16x16.png]freesurfer_recon-all_1.py.out


发件人: Quanjiang Liu
发送时间: 2024年6月27日 2:11
收件人: freesurfer@nmr.mgh.harvard.edu 
主题: The file absence problem of the recon-all -all output

  Hi, I ran the recon-all -all command successfully. But the lh.seghead and 
rh.seghead didn't appear in my output folder. The attachment is the process 
record. Can you help to solve it?
  Sorry to bother.
Best
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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