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
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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. 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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <o.batuhanerkat@gmail.commailto:o.batuhanerkat@gmail.com> Sent: Tuesday, November 27, 2018 10:28:23 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: batuhan.erkat@umram.bilkent.edu.trmailto:batuhan.erkat@umram.bilkent.edu.tr; astevens@nmr.mgh.harvard.edumailto:astevens@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
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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.commailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat <o.batuhanerkat@gmail.commailto:o.batuhanerkat@gmail.com> Sent: Wednesday, November 21, 2018 12:01:53 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: batuhan.erkat@umram.bilkent.edu.trmailto:batuhan.erkat@umram.bilkent.edu.tr; astevens@nmr.mgh.harvard.edumailto:astevens@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, 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.edumailto: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?
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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