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." <dgr...@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, k3...@free.fr 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 > 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
