what is the terminal output for mris_seg2annot? On 06/05/2015 06:12 PM, Matthieu Vanhoutte wrote: > > I tried it but gave me a black surface. > > Le 6 juin 2015 00:06, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> a écrit : > > Try it with 0 0 0 instead of 128 128 128 > > On 06/05/2015 07:44 AM, Matthieu Vanhoutte wrote: > > Dear FreeSurfer's experts, > > > > I would like to visualize on freeview two overlays on fsaverage > > cortical surface. > > > > I have used the code below found on the mailing list : > > > > /mri_binarize --i sig1.mgh --min 0.1 --binval 1 --o sig1_th.mgh > > mri_binarize --i sig2.mgh --min 0.1 --binval 2 --o sig2_th.mgh > > > > / > > /fscalc sig1_th.mgh add sig2_th.mgh --o sig1_sig2.mgh > > > > mris_seg2annot --seg sig1_sig2.mgh --ctab sig1_sig2_LUT.txt --s > > fsaverage --h lh --o sig1_sig2.annot/ > > > > with sig1_sig2.annot defined as below : > > > > #No. Label Name: R G B A > > > > 0 Unknown 128 128 128 0 > > 1 sig1 70 130 180 0 > > 2 sig2 245 245 245 0 > > 3 Overlay_sig1_sig2 205 62 78 0 > > > > My problem is that I'd like to view my cortical suface with binary > > curvature where there is no value (=0). Could I specify the unknown > > label (0) to be transparent or anything that could solve the mater ? > > > > Best regards, > > > > Matthieu > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
