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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <o.batuhanerkat@gmail.com>
Sent: Saturday, December 1, 2018 9:52:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.erkat@umram.bilkent.edu.tr; astevens@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 <BRDIAMOND@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <o.batuhanerkat@gmail.com>
Sent: Friday, November 30, 2018 12:49:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.erkat@umram.bilkent.edu.tr; astevens@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 <BRDIAMOND@mgh.harvard.edu> wrote:

Can you please upload the BE2_T1.nii?


Bram

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <o.batuhanerkat@gmail.com>
Sent: Thursday, November 29, 2018 12:35:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.erkat@umram.bilkent.edu.tr; astevens@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 <BRDIAMOND@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <o.batuhanerkat@gmail.com>
Sent: Tuesday, November 27, 2018 10:28:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.erkat@umram.bilkent.edu.tr; astevens@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.batuhanerkat@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 <BRDIAMOND@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <o.batuhanerkat@gmail.com>
Sent: Wednesday, November 21, 2018 12:01:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.erkat@umram.bilkent.edu.tr; astevens@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 <BRDIAMOND@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?


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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


-- 
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


-- 
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


-- 
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center

Bilkent University
Ankara, 06800
Turkey