Instead of using an echo this time, I inputted the direct paths straight into the command line. I am in the tcsh shell.
On Thu, Sep 10, 2015 at 10:25 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > did you try putting an echo in front to see how it expands? What shell are > you using? > > On Thu, 10 Sep 2015, Sam Zorowitz wrote: > > Hi Bruce, >> Thank you for the reply. I had been running it through python. After >> running the command from the >> command line, however, I am still receiving the same error. >> >> Best, >> Sam >> >> On Thu, Sep 10, 2015 at 9:00 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Sam >> >> are you running this from a unix/linux command line? The >> usually >> means >> matlab. In any case, it looks like $CTAB is not being expanded by >> the >> shell. Try using echo to see what the actual command is. >> >> cheers >> Bruce >> >> >> On Thu, 10 Sep 2015, >> Sam Zorowitz wrote: >> >> > Hi all, >> > >> > I am trying to make a custom annotation file. In doing so, I have >> created a custom color >> lookup table. >> > I have attached the CLUT. I run the following command: >> > >> > >> mris_label2annot --subject $SUBJ --hemi $HEMI --ctab $CTAB --a >> $OUT --l label_1 --l >> label_2 ... --l >> > label_n >> > >> > And I receive the following error: >> > >> > >> CTABreadASCII($CTAB): badly formed file >> > >> Reading ctab $CTAB >> > >> ERROR: reading $CTAB >> > >> > I have searched the archives for similar problems. The only >> previous hit I could find is >> someone who >> > had made the CLUT on Windows -- but I have made mine on Unix and >> the character encoding >> is us-ascii. >> > >> > Any advice from the listserv? Thanks! >> > >> > -Sam >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> 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 > > > 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 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.
