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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-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：
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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
________________________________ 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：
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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
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
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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.cnmailto:sjiang13@fudan.edu.cn
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