Recon-all - mghRead could not read rawavg.mgz - Freesurfer

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Problem in Installing FreeSurfer...

Diamond, Bram Ryder

21 Nov 2018 21 Nov '18

11:31 a.m.

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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Batuhan Erkat

21 Nov 21 Nov

12:01 p.m.

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?

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

Batuhan Erkat

24 Nov 24 Nov

12:33 p.m.

External Email - Use Caution

Hello again,

Could you reach the files?

Best, Batuhan

On Wed, Nov 21, 2018 at 8:01 PM Batuhan Erkat o.batuhanerkat@gmail.com 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 < 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

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

Diamond, Bram Ryder

26 Nov 26 Nov

2:23 p.m.

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

________________________________ 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,

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

_______________________________________________ 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

Batuhan Erkat

27 Nov 27 Nov

4:47 a.m.

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?

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

Batuhan Erkat

10:28 a.m.

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.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.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?

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

Diamond, Bram Ryder

29 Nov 29 Nov

9:35 a.m.

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

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Batuhan Erkat o.batuhanerkat@gmail.com Sent: Tuesday, November 27, 2018 10:28:23 AM 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

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

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

________________________________ 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

External Email - Use Caution

Hi Bram,

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

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

MSc Candidate

Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center

Bilkent University Ankara, 06800 Turkey

Batuhan Erkat

12:35 p.m.

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 < 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.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat < o.batuhanerkat@gmail.com> *Sent:* Tuesday, November 27, 2018 10:28:23 AM *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
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.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.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?

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

Diamond, Bram Ryder

30 Nov 30 Nov

12:45 p.m.

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

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 <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> wrote:

Thanks for your patience! I'll be updating our wiki documentation to be more clear.

Bram

________________________________ 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

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.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

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

External Email - Use Caution

Hi Bram,

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

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

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

Batuhan Erkat

12:49 p.m.

External Email - Use Caution

Done

On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> wrote:

...

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
    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 < 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.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat < o.batuhanerkat@gmail.com> *Sent:* Tuesday, November 27, 2018 10:28:23 AM *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
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.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.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?

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

Diamond, Bram Ryder

5:53 p.m.

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Batuhan Erkat o.batuhanerkat@gmail.com Sent: Friday, November 30, 2018 12:49:42 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

Done

On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> wrote:

Can you please upload the BE2_T1.nii?

Bram

________________________________ 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: Thursday, November 29, 2018 12:35:06 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

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 <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> wrote:

Thanks for your patience! I'll be updating our wiki documentation to be more clear.

Bram

________________________________ 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

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.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

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

External Email - Use Caution

Hi Bram,

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

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

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

MSc Candidate

Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research Center

Bilkent University Ankara, 06800 Turkey

Batuhan Erkat

1 Dec 1 Dec

9:52 a.m.

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 < BRDIAMOND@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat < o.batuhanerkat@gmail.com> *Sent:* Friday, November 30, 2018 12:49:42 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
Done

On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder < BRDIAMOND@mgh.harvard.edu> wrote:

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
    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 < 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.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Batuhan Erkat < o.batuhanerkat@gmail.com> *Sent:* Tuesday, November 27, 2018 10:28:23 AM *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
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.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.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?

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

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

Diamond, Bram Ryder

3 Dec 3 Dec

11:01 a.m.

I'm not sure why there is no error with the mri_convert function, but it somehow took in your BE2_T1.nii and creating a corrupted 001.mgz. The rawavg.mgz is just a copy of the 001.mgz, so it's no surprise that it has the same issues. You only get an error when recon-all attempts to run mri_convert on the rawavg.mgz.

The corrupted 001.mgz is only 8K - it should be more like 12M. I can't open it in Matlab with MRIread to see what might have gone wrong. I'm not sure what the problem is, but it is definitely local to whatever machine you are using to run recon-all. I've run the nifty you uploaded through recon-all using freesurfer 5.3 without an issue on my machine.

Please let me know if downloading freesurfer again fixes the issue.

Best,

Bram

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Batuhan Erkat o.batuhanerkat@gmail.com Sent: Saturday, December 1, 2018 9:52:34 AM 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

Best, Batuhan

On Sat, Dec 1, 2018 at 12:54 AM Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@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-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: Friday, November 30, 2018 12:49:42 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

External Email - Use Caution

Done

On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> wrote:

Can you please upload the BE2_T1.nii?

Bram

________________________________ 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: Thursday, November 29, 2018 12:35:06 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

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 <BRDIAMOND@mgh.harvard.edumailto:BRDIAMOND@mgh.harvard.edu> wrote:

Thanks for your patience! I'll be updating our wiki documentation to be more clear.

Bram

________________________________ 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

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.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

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

External Email - Use Caution

Hi Bram,

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

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

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

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

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freesurfer@nmr.mgh.harvard.edu

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Batuhan Erkat
Diamond, Bram Ryder