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, [email protected] wrote: > External Email - Use Caution > > 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." <[email protected]> > À: [email protected] > 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, [email protected] wrote: >> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
