...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
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I will ask our admin to do so. I also don't have any problems on my personal
computer, so my T1 image should be fine, but the problem starts
:42 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
>
>
> External Email - Use Caution
>
> Done
>
> On Fri, Nov 30, 2018
@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
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Done
On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder
mailto:brdiam...@mgh.harvard.edu>>
Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <
&
...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
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Hi Bram,
I finally did it, thank you for your help, and sorry about my noobity!
ftp> put BE2.tar.xz
local: BE2.tar.xz remote: BE2.tar.xz
200 PORT command successful. Consi
u <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <
> o.batuhaner...@gmail.com>
> *Sent:* Tuesday, November 27, 2018 10:28:23 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
> *Subje
nmr.mgh.harvard.edu>
Cc:
batuhan.er...@umram.bilkent.edu.tr<mailto:batuhan.er...@umram.bilkent.edu.tr>;
astev...@nmr.mgh.harvard.edu<mailto:astev...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
External Email - Use Caution
Hi Bram,
t;> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <
>> o.batuhaner...@gmail.com>
>> *Sent:* Wednesday, November 21, 2018 12:01:53 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Cc:* batuhan.er...@umram.bilkent.edu.tr; astev...@nmr
.@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <
> o.batuhaner...@gmail.com>
> *Sent:* Wednesday, November 21, 2018 12:01:53 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Cc:* batuhan.er...@umram.bilkent.edu.tr; as
; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
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Hi Bram,
I uploaded all the files, including my input image and recon-all scripts. As
you can see, there are no errors for mri_convert
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Hello again,
Could you reach the files?
Best,
Batuhan
On Wed, Nov 21, 2018 at 8:01 PM Batuhan Erkat
wrote:
> Hi Bram,
>
> I uploaded all the files, including my input image and recon-all scripts.
> As you can see, there are no errors for
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Hi Bram,
I uploaded all the files, including my input image and recon-all scripts.
As you can see, there are no errors for mri_convert, but there is for
mghRead(). If you inspect the 001.mgz and rawavg.mgz files, you'll realize
that they are corrupted
Hi Batuhan,
Can you please upload the BE2 subject data using our ftp file exchange and let
me know the exact command and terminal output when you ran mri_convert?
Info on our ftp file exchange:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Thanks,
Bram
Bram R. Diamond, BSc
wow, I have no idea. Can you send us the .nii file and we will try? What
machine is it failing on and does it print any error messages during
conversion? Can you send us the full command line and terminal output of
the mri_convert command that fails?
cheers
Bruce
On Tue, 20 Nov 2018, Batuhan
Hi Batuhan
what is the size of the rawavg.mgz file? Can you run mri_info on it? How
did you create the 001.mgz? Rerunning recon-all won't help if the 001.mgz
is already corrupted - you will need to regenerate it. That fact that we
can't even read slice 0 suggests there is something badly
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Yes, unfortunately same error reoccurs in three different machines. I
talked with some people at the research center, they claimed that it could
be due to high load. However, I tried again while the average load was at
5% (via top command), the issue
Probably it was interrupted and the file as not completely written, or you ran
out of space on the disk. If you start over, does it continue to happen?
On 11/16/18 4:15 PM, Batuhan Erkat wrote:
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Hello,
I am using FreeSurfer solely for reconstruction. I am
External Email - Use Caution
Hello,
I am using FreeSurfer solely for reconstruction. I am having an issue I
didn't have a month ago, right at the beginning of reconstruction pipeline.
I am using FreeSurfer v5.3.0 on an Ubuntu 14.04 server. Based on some
search and thinking, I
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