External Email - Use Caution Done
On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder < brdiam...@mgh.harvard.edu> wrote: > Can you please upload the BE2_T1.nii? > > > Bram > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat < > o.batuhaner...@gmail.com> > *Sent:* Thursday, November 29, 2018 12:35:06 PM > *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 > > 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> 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 < > 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> > 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> 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 < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat < > o.batuhaner...@gmail.com> > *Sent:* Wednesday, November 21, 2018 12:01:53 PM > *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 > > 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> 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 > 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 > > > > -- > > 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
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