I'm not sure why there is no error with the mri_convert function, but it
somehow took in your BE2_T1.nii and creating a corrupted 001.mgz. The
rawavg.mgz is just a copy of the 001.mgz, so it's no surprise that it has the
same issues. You only get an error when recon-all attempts to run mri_convert
on the rawavg.mgz.
The corrupted 001.mgz is only 8K - it should be more like 12M. I can't open it
in Matlab with MRIread to see what might have gone wrong. I'm not sure what the
problem is, but it is definitely local to whatever machine you are using to run
recon-all. I've run the nifty you uploaded through recon-all using freesurfer
5.3 without an issue on my machine.
Please let me know if downloading freesurfer again fixes the issue.
Best,
Bram
Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical 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
<o.batuhaner...@gmail.com>
Sent: Saturday, December 1, 2018 9:52:34 AM
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
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 at mri_convert
function, which surprisingly gives no error. Is it possible for you to look at
the 001.mgz and rawavg.mgz files and see what could be the problem with the
mri_convert function?
Best,
Batuhan
On Sat, Dec 1, 2018 at 12:54 AM Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu<mailto:brdiam...@mgh.harvard.edu>> wrote:
It's strange, but I'm not having the same issue. Can you try downloading 5.3
again and see if that fixes your issue?
Bram
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Batuhan Erkat
<o.batuhaner...@gmail.com<mailto:o.batuhaner...@gmail.com>>
Sent: Friday, November 30, 2018 12:49:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@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
Done
On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu<mailto:brdiam...@mgh.harvard.edu>> wrote:
Can you please upload the BE2_T1.nii?
Bram
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Batuhan Erkat
<o.batuhaner...@gmail.com<mailto:o.batuhaner...@gmail.com>>
Sent: Thursday, November 29, 2018 12:35:06 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@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,
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. Consider using PASV.
150 Ok to send data.
226 Transfer complete.
61572 bytes sent in 0.15 secs (402.3777 kB/s)
Best regards,
Batuhan
On Thu, Nov 29, 2018 at 5:36 PM Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu<mailto:brdiam...@mgh.harvard.edu>> wrote:
I can't see any of your data. The problem is likely that you are feeding the
full file path. Try using just the file name without the path. First cd to your
data directory, then log on to the freesurfer FTP file exchange and follow the
instructions on our wiki.
Thanks for your patience! I'll be updating our wiki documentation to be more
clear.
Bram
Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Batuhan Erkat
<o.batuhaner...@gmail.com<mailto:o.batuhaner...@gmail.com>>
Sent: Tuesday, November 27, 2018 10:28:23 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@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
I tried to put the subject folder in tar.xz format for ease, this is what I get:
ftp> put /home/gorkem/output/BE2.tar.xz
local: /home/gorkem/output/BE2.tar.xz remote: /home/gorkem/output/BE2.tar.xz
200 PORT command successful. Consider using PASV.
553 Could not create file.
Best,
Batuhan
On Tue, Nov 27, 2018 at 12:47 PM Batuhan Erkat
<o.batuhaner...@gmail.com<mailto:o.batuhaner...@gmail.com>> wrote:
Hello Bram,
I just followed the guideline at FTPFileExchange, put them to transfer/incoming.
Files I put are:
001.mgz
rawavg.mgz
build-stamp.txt
recon-all-status.log
recon-all.cmd
recon-all.env
recon-all.error
recon-all.local-copy
recon-all.log
error.log
I tried to create a folder, but of course I don't have permission. If you can
open a folder named Batuhan, or something like that, I can put them there.
Also, I tried and couldn't put my subject folder directly via Filezilla or the
terminal.
Best,
Batuhan
On Mon, Nov 26, 2018 at 10:23 PM Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu<mailto:brdiam...@mgh.harvard.edu>> wrote:
Hi Batuhan,
I'm trying to access the files now. What is the name of the files/directory
you uploaded? I'm not sure they transferred.
Thanks,
Bram
Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Batuhan Erkat
<o.batuhaner...@gmail.com<mailto:o.batuhaner...@gmail.com>>
Sent: Wednesday, November 21, 2018 12:01:53 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@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,
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 and probably that's why mghRead fails to read rawavg.mgz.
Can you see the files, did I do the file transmission correctly?
Best,
Batuhan
On Wed, Nov 21, 2018 at 7:32 PM Diamond, Bram Ryder
<brdiam...@mgh.harvard.edu<mailto:brdiam...@mgh.harvard.edu>> wrote:
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
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598
_______________________________________________
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--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
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--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
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--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
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--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
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--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
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