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 < brdiam...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat < > o.batuhaner...@gmail.com> > *Sent:* Friday, November 30, 2018 12:49:42 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 > > 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 > 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
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 < 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 > 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 cor
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 > 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 > > __
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 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
Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
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 < 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
External Email - Use Caution Hello again, Could you reach the files? Best, Batuhan On Wed, Nov 21, 2018 at 8:01 PM Batuhan Erkat wrote: > 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 > > -- 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
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
Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
External Email - Use Caution
Yes, unfortunately same error reoccurs in three different machines. I
talked with some people at the research center, they claimed that it could
be due to high load. However, I tried again while the average load was at
5% (via top command), the issue persists. Do you have any clue what might
be the underlying problem? A necessary bug fix we could have missed etc.?
Batuhan
On Sat, Nov 17, 2018 at 12:11 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Probably it was interrupted and the file as not completely written, or you
> ran out of space on the disk. If you start over, does it continue to happen?
>
> On 11/16/18 4:15 PM, Batuhan Erkat wrote:
>
> External Email - Use Caution
> Hello,
>
> I am using FreeSurfer solely for reconstruction. I am having an issue I
> didn't have a month ago, right at the beginning of reconstruction pipeline.
> I am using FreeSurfer v5.3.0 on an Ubuntu 14.04 server. Based on some
> search and thinking, I guess that mghread is not able to read rawavg.mgz
> either there is a bug with the mghread or the data gets corrupted during
> mri_convert, because when I inspect the T1.nii images, there seems to be
> nothing wrong. Furthermore, I tried recon-all command on the anatomical
> images I reconstructed a month ago without any error (which means they were
> totally okay), but not surprisingly I received the same error message when
> I tried to conduct recon-all on them:
> *mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz):
> could not read 229376 bytes at slice 0*
> I also included an error log, and the full terminal output where I bolded
> out the problematic lines. Also, I am not sure how related it is with my
> issue but there are some warnings from perl as well.
>
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /usr/local/freesurfer
> FSFAST_HOME /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /auto/data/batuhan/output
> MNI_DIR /usr/local/freesurfer/mni
> batuhan@chimere:~$ recon-all -i /auto/data/batuhan/output/BE_T1.nii -s BE
> -all
> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /auto/data/batuhan/output
> Actual FREESURFER_HOME /usr/local/freesurfer
> Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC
> 2016 x86_64 x86_64 x86_64 GNU/Linux
> perl: warning: Setting locale failed.
> perl: warning: Please check that your locale settings:
> LANGUAGE = "en_US:en",
> LC_ALL = (unset),
> LC_PAPER = "tr_TR.UTF-8",
> LC_ADDRESS = "tr_TR.UTF-8",
> LC_MONETARY = "tr_TR.UTF-8",
> LC_NUMERIC = "tr_TR.UTF-8",
> LC_TELEPHONE = "tr_TR.UTF-8",
> LC_IDENTIFICATION = "tr_TR.UTF-8",
> LC_MEASUREMENT = "tr_TR.UTF-8",
> LC_TIME = "tr_TR.UTF-8",
> LC_NAME = "tr_TR.UTF-8",
> LANG = "C"
> are supported and installed on your system.
> perl: warning: Falling back to the standard locale ("C").
> /auto/data/batuhan/output/BE
>
> mri_convert /auto/data/batuhan/output/BE_T1.nii
> /auto/data/batuhan/output/BE/mri/orig/001.mgz
>
> mri_convert /auto/data/batuhan/output/BE_T1.nii
> /auto/data/batuhan/output/BE/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from /auto/data/batuhan/output/BE_T1.nii...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0, -1, 0)
> j_ras = (0, 0, 1)
> k_ras = (1, 0, 0)
> writing to /auto/data/batuhan/output/BE/mri/orig/001.mgz...
> #
> #@# MotionCor Fri Nov 16 23:43:47 +03 2018
> Found 1 runs
> /auto/data/batuhan/output/BE/mri/orig/001.mgz
> Checking for (invalid) multi-frame inputs...
> WARNING: only one run found. This is OK, but motion
> correction cannot be performed on one run, so I'll
> copy the run to rawavg and continue.
>
> cp /auto/data/batuhan/output/BE/mri/orig/001.mgz
> /auto/data/batuhan/output/BE/mri/rawavg.mgz
>
> /auto/data/batuhan/output/BE
>
> mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz
> /auto/data/batuhan/output/BE/mri/orig.mgz --conform
>
>
>
>
>
> *mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz
> /auto/data/batuhan/output/BE/mri/orig.mgz --conform
> mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376
> bytes at slice 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
> Exp $ reading from /au
[Freesurfer] Recon-all - mghRead could not read rawavg.mgz
External Email - Use Caution
Hello,
I am using FreeSurfer solely for reconstruction. I am having an issue I
didn't have a month ago, right at the beginning of reconstruction pipeline.
I am using FreeSurfer v5.3.0 on an Ubuntu 14.04 server. Based on some
search and thinking, I guess that mghread is not able to read rawavg.mgz
either there is a bug with the mghread or the data gets corrupted during
mri_convert, because when I inspect the T1.nii images, there seems to be
nothing wrong. Furthermore, I tried recon-all command on the anatomical
images I reconstructed a month ago without any error (which means they were
totally okay), but not surprisingly I received the same error message when
I tried to conduct recon-all on them:
*mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz):
could not read 229376 bytes at slice 0*
I also included an error log, and the full terminal output where I bolded
out the problematic lines. Also, I am not sure how related it is with my
issue but there are some warnings from perl as well.
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /auto/data/batuhan/output
MNI_DIR /usr/local/freesurfer/mni
batuhan@chimere:~$ recon-all -i /auto/data/batuhan/output/BE_T1.nii -s BE
-all
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /auto/data/batuhan/output
Actual FREESURFER_HOME /usr/local/freesurfer
Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = "en_US:en",
LC_ALL = (unset),
LC_PAPER = "tr_TR.UTF-8",
LC_ADDRESS = "tr_TR.UTF-8",
LC_MONETARY = "tr_TR.UTF-8",
LC_NUMERIC = "tr_TR.UTF-8",
LC_TELEPHONE = "tr_TR.UTF-8",
LC_IDENTIFICATION = "tr_TR.UTF-8",
LC_MEASUREMENT = "tr_TR.UTF-8",
LC_TIME = "tr_TR.UTF-8",
LC_NAME = "tr_TR.UTF-8",
LANG = "C"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
/auto/data/batuhan/output/BE
mri_convert /auto/data/batuhan/output/BE_T1.nii
/auto/data/batuhan/output/BE/mri/orig/001.mgz
mri_convert /auto/data/batuhan/output/BE_T1.nii
/auto/data/batuhan/output/BE/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /auto/data/batuhan/output/BE_T1.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to /auto/data/batuhan/output/BE/mri/orig/001.mgz...
#
#@# MotionCor Fri Nov 16 23:43:47 +03 2018
Found 1 runs
/auto/data/batuhan/output/BE/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /auto/data/batuhan/output/BE/mri/orig/001.mgz
/auto/data/batuhan/output/BE/mri/rawavg.mgz
/auto/data/batuhan/output/BE
mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz
/auto/data/batuhan/output/BE/mri/orig.mgz --conform
*mri_convert /auto/data/batuhan/output/BE/mri/rawavg.mgz
/auto/data/batuhan/output/BE/mri/orig.mgz --conform
mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376
bytes at slice 0$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp $reading from /auto/data/batuhan/output/BE/mri/rawavg.mgz...Invalid
argument*
Linux chimere 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC
2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s BE exited with ERRORS at Fri Nov 16 23:43:50 +03 2018
For more details, see the log file
/auto/data/batuhan/output/BE/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thank you.
Best regards,
O. Batuhan Erkat
--
MSc Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM) &
Aysel Sabuncu Brain Research Center
Bilkent University
Ankara, 06800
Turkey
mghRead(/auto/data/batuhan/output/BE/mri/rawavg.mgz): could not read 229376 bytes at slice 0
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