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
<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
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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
--
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
