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