External Email - Use Caution
Hi FS team,
I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not able to precess, I always get the following error during "mri_convert" procedure (before calling recon-all), I also wrote the last command that produces this error:
fsdcmdecompress --i freesurfer_18/6858304 --o /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out sh: 1: Syntax error: Bad fd number
After some investigations, it looks it is related to the way standard outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing by the way). It looks like ">&" redirection is not a correct syntax in bash (the shell I am using), so I tried with others but unfortunately none of them worked so far (zsh, tcsh, csh, sh).
Do you have any recommendation for the way to use "mri_convert" tool? or any other tool that could convert DICOM to nifty efficiently?
Thanks for your feedbacks.
Regards, Florent
What shell are you using? Try using cshell or tcshell to see if it works.
On 10/2/18 4:56 AM, k3ops@free.fr wrote:
External Email - Use CautionHi FS team,
I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not able to precess, I always get the following error during "mri_convert" procedure (before calling recon-all), I also wrote the last command that produces this error:
fsdcmdecompress --i freesurfer_18/6858304 --o /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out sh: 1: Syntax error: Bad fd number
After some investigations, it looks it is related to the way standard outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing by the way). It looks like ">&" redirection is not a correct syntax in bash (the shell I am using), so I tried with others but unfortunately none of them worked so far (zsh, tcsh, csh, sh).
Do you have any recommendation for the way to use "mri_convert" tool? or any other tool that could convert DICOM to nifty efficiently?
Thanks for your feedbacks.
Regards, Florent
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I am using bash shell but I tried with many others as mentioned in my first post (zsh, tcsh, csh, sh) and nothing worked so far...
----- Mail original ----- De: "Douglas N. Greve,Ph.D." DGREVE@mgh.harvard.edu À: freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 2 Octobre 2018 15:18:14 Objet: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series
What shell are you using? Try using cshell or tcshell to see if it works.
On 10/2/18 4:56 AM, k3ops@free.fr wrote:
External Email - Use CautionHi FS team,
I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not able to precess, I always get the following error during "mri_convert" procedure (before calling recon-all), I also wrote the last command that produces this error:
fsdcmdecompress --i freesurfer_18/6858304 --o /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out sh: 1: Syntax error: Bad fd number
After some investigations, it looks it is related to the way standard outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing by the way). It looks like ">&" redirection is not a correct syntax in bash (the shell I am using), so I tried with others but unfortunately none of them worked so far (zsh, tcsh, csh, sh).
Do you have any recommendation for the way to use "mri_convert" tool? or any other tool that could convert DICOM to nifty efficiently?
Thanks for your feedbacks.
Regards, Florent
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, I meant to change your default shell. That command is being run using the system() command from inside of a c-program, which undoubtedly starts your default shell. Just see if it works.
On 10/02/2018 10:36 AM, k3ops@free.fr wrote:
External Email - Use CautionI am using bash shell but I tried with many others as mentioned in my first post (zsh, tcsh, csh, sh) and nothing worked so far...
----- Mail original ----- De: "Douglas N. Greve,Ph.D." DGREVE@mgh.harvard.edu À: freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 2 Octobre 2018 15:18:14 Objet: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series
What shell are you using? Try using cshell or tcshell to see if it works.
On 10/2/18 4:56 AM, k3ops@free.fr wrote:
External Email - Use CautionHi FS team,
I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not able to precess, I always get the following error during "mri_convert" procedure (before calling recon-all), I also wrote the last command that produces this error:
fsdcmdecompress --i freesurfer_18/6858304 --o /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out sh: 1: Syntax error: Bad fd number
After some investigations, it looks it is related to the way standard outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing by the way). It looks like ">&" redirection is not a correct syntax in bash (the shell I am using), so I tried with others but unfortunately none of them worked so far (zsh, tcsh, csh, sh).
Do you have any recommendation for the way to use "mri_convert" tool? or any other tool that could convert DICOM to nifty efficiently?
Thanks for your feedbacks.
Regards, Florent
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It may be complaining about >& for redirection. Try using 2>&1 instead.
On Oct 2, 2018, at 4:56 AM, k3ops@free.frmailto:k3ops@free.fr wrote:
sh: 1: Syntax error: Bad fd number
The command is being run from inside of a C-file using the system command, so there is no way for them to change it
On 10/02/2018 01:43 PM, Dicamillo, Robert wrote:
It may be complaining about >& for redirection. Try using 2>&1 instead.
On Oct 2, 2018, at 4:56 AM, k3ops@free.fr mailto:k3ops@free.fr wrote:
sh: 1: Syntax error: Bad fd number
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Dicamillo, Robert -
Greve, Douglas N.,Ph.D. -
k3ops＠free.fr