Can you send the terminal output and/or the log file? On 08/22/2018 09:49 AM, Nada Naguib wrote: > > External Email - Use Caution > > Hello, thank you for your response, yes My terminal is in the tcsh > shell so I’m not sure why it’s not working > > Nada > > > On Aug 22, 2018, at 3:22 PM, Adam Martersteck <acmar...@gmail.com > <mailto:acmar...@gmail.com>> wrote: > >> External Email - Use Caution >> >> Are you sure you're terminal is setup in tcsh or csh? If you're using >> bash instead, you want "export SUBJECTS_DIR=/project/bil/Nada" >> Take a look at: >> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac or >> https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux to >> see if you may have missed something. >> >> On Wed, Aug 22, 2018 at 4:37 AM Nada Naguib <nad...@bu.edu >> <mailto:nad...@bu.edu>> wrote: >> >> External Email - Use Caution >> >> Hello, >> >> I have been using bbregister in this format >> >> bbregister —mov dkti4d.nii —s NewT2out —init-fsl —bold —lea >> register.lta >> >> NewT2out is the output of the free surfer processing on the T1 >> image and dkti4d.nii is the template file I want to use for the >> registration. >> >> it has worked before but now there is a new error >> >> ERROR: cannot find NewT2out in >> /project/iconic/apps/freesurfer/5.3.0/install/subjects >> >> even though I have already ran the command: >> >> setenv SUBJECTS_DIRECTORY /project/bil/Nada >> >> >> This path is where both NewT2out and dkti4d.nii are located. >> >> I don’t understand what is going wrong >> >> Best >> Nada >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent >> to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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