External Email - Use Caution        

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
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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