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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.igles...@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
--
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-boun...@nmr.mgh.harvard.edu> on behalf of 姜时泽
<jiangshize1...@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.igles...@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/
From:freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of 姜时泽
<jiangshize1...@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.igles...@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-boun...@nmr.mgh.harvard.edu> on behalf of 姜时泽
<jiangshize1...@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
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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: sjian...@fudan.edu.cn
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