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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

在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk> 写道：

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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

 

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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

 

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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：

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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

http://www.jeiglesias.com

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

 

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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

 

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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

 

-- 

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.cn