Hi Linda, check your color table to make sure that the entry indices are in numerical order without a gap (i,e 1 2 3 4 5 is ok, but 1 3 4 5 would not be). doug
On 12/18/2012 11:49 AM, Linda Douw wrote: > Hi experts, > > I have a bunch of custom-made labels (from the ConnectomeMapper software) > that I want to put into a single annotation file. Therefore, I create a > color-lookup table and use mris_label2annot as follows: > > mris_label2annot --s fsaveragec --h lh --ctab lh_laus500_clut_new.txt --a > laus500_fixed_newest --l $LABEL_DIR/lh.bankssts_1.label --l > $LABEL_DIR/lh.bankssts_2.label --l $LABEL_DIR/lh.bankssts_3.label ... etc > for all labels > > Then, I try to load this annotation with tksurfer, but some errors come up > (see below). What do these error messages mean? Could it have something to > do with some vertices not having a label assigned to them? > The annotation does look okay on tksurfer, but I run into problems later > when using it, so I do need to work out why these errors come up. > > Thanks, > Linda > > tksurfer fsaveragec lh inflated -annotation laus500_fixed_newest > subject is fsaveragec > hemi is lh > surface is inflated > surfer: current subjects dir: /cluster/neuromind/douw/scans/controls > surfer: in dir with "scripts" in name > surfer: session root data dir ($session) set to: > surfer: /autofs/cluster/neuromind/douw > checking for nofix files in 'inflated' > Reading image info (/cluster/neuromind/douw/scans/controls/fsaveragec) > Reading /cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz > surfer: Reading header info from > /cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz > surfer: vertices=163842, faces=327680 > reading colortable from annotation file... > colortable with 502 entries read (originally > /cluster/neuromind/douw/scans/lh_laus500_clut_new.txt) > Found embedded color table in annotation. > Warning: vertex 206 with annotation 100e251 - out of range! > Warning: vertex 1280 with annotation 100e251 - out of range! > Warning: vertex 2371 with annotation 100e251 - out of range! > Warning: vertex 2372 with annotation 100e251 - out of range! > Warning: vertex 5282 with annotation 100e251 - out of range! > Warning: vertex 5283 with annotation 100e251 - out of range! > Warning: vertex 5284 with annotation 100e251 - out of range! > Warning: vertex 5285 with annotation 100e251 - out of range! > Warning: vertex 6914 with annotation 100e251 - out of range! > Warning: vertex 6915 with annotation 100e251 - out of range! > Warning: vertex 9669 with annotation 100e251 - out of range! > Warning: vertex 9670 with annotation 100e251 - out of range! > Warning: vertex 9671 with annotation 100e251 - out of range! > Warning: vertex 9672 with annotation 100e251 - out of range! > Warning: vertex 9673 with annotation 100e251 - out of range! > Warning: vertex 11176 with annotation 100e251 - out of range! > Warning: vertex 11178 with annotation 100e251 - out of range! > Warning: vertex 12962 with annotation 100e251 - out of range! > Warning: vertex 12963 with annotation 100e251 - out of range! > Warning: vertex 12964 with annotation 100e251 - out of range! > Warning: vertex 12965 with annotation 100e251 - out of range! > Warning: vertex 15365 with annotation 100e251 - out of range! > Warning: vertex 21604 with annotation 100e251 - out of range! > Warning: vertex 21605 with annotation 100e251 - out of range! > Warning: vertex 21606 with annotation 100e251 - out of range! > Warning: vertex 21607 with annotation 100e251 - out of range! > Warning: vertex 21608 with annotation 100e251 - out of range! > Warning: vertex 21609 with annotation 100e251 - out of range! > Warning: vertex 21610 with annotation 100e251 - out of range! > Warning: vertex 21611 with annotation 100e251 - out of range! > Warning: vertex 21612 with annotation 100e251 - out of range! > Warning: vertex 21613 with annotation 100e251 - out of range! > Warning: vertex 21614 with annotation 100e251 - out of range! > Warning: vertex 21615 with annotation 100e251 - out of range! > Warning: vertex 21616 with annotation 100e251 - out of range! > Warning: vertex 21617 with annotation 100e251 - out of range! > Warning: vertex 21618 with annotation 100e251 - out of range! > Warning: vertex 27939 with annotation 100e251 - out of range! > Warning: vertex 27940 with annotation 100e251 - out of range! > Warning: vertex 27941 with annotation 100e251 - out of range! > Warning: vertex 27942 with annotation 100e251 - out of range! > Warning: vertex 27943 with annotation 100e251 - out of range! > Warning: vertex 27944 with annotation 100e251 - out of range! > Warning: vertex 27945 with annotation 100e251 - out of range! > Warning: vertex 27946 with annotation 100e251 - out of range! > Warning: vertex 27947 with annotation 100e251 - out of range! > Warning: vertex 28990 with annotation 100e251 - out of range! > Warning: vertex 28991 with annotation 100e251 - out of range! > Warning: vertex 31491 with annotation 100e251 - out of range! > Warning: vertex 31493 with annotation 100e251 - out of range! > Warning: vertex 31494 with annotation 100e251 - out of range! > Warning: vertex 31495 with annotation 100e251 - out of range! > Warning: vertex 31496 with annotation 100e251 - out of range! > Warning: vertex 31497 with annotation 100e251 - out of range! > Warning: vertex 39242 with annotation 100e251 - out of range! > Warning: vertex 39243 with annotation 100e251 - out of range! > Warning: vertex 39245 with annotation 100e251 - out of range! > Warning: vertex 39246 with annotation 100e251 - out of range! > Warning: vertex 39247 with annotation 100e251 - out of range! > Warning: vertex 39248 with annotation 100e251 - out of range! > Warning: vertex 39249 with annotation 100e251 - out of range! > Warning: vertex 39250 with annotation 100e251 - out of range! > Warning: vertex 39251 with annotation 100e251 - out of range! > Warning: vertex 39252 with annotation 100e251 - out of range! > Warning: vertex 39253 with annotation 100e251 - out of range! > Warning: vertex 39254 with annotation 100e251 - out of range! > Warning: vertex 39256 with annotation 100e251 - out of range! > Warning: vertex 41896 with annotation 100e251 - out of range! > Warning: vertex 41897 with annotation 100e251 - out of range! > Warning: vertex 41898 with annotation 100e251 - out of range! > Warning: vertex 43682 with annotation 100e251 - out of range! > Warning: vertex 43683 with annotation 100e251 - out of range! > Warning: vertex 43684 with annotation 100e251 - out of range! > Warning: vertex 43685 with annotation 100e251 - out of range! > Warning: vertex 52322 with annotation 100e251 - out of range! > Warning: vertex 52324 with annotation 100e251 - out of range! > Warning: vertex 52325 with annotation 100e251 - out of range! > Warning: vertex 52326 with annotation 100e251 - out of range! > Warning: vertex 52327 with annotation 100e251 - out of range! > Warning: vertex 52328 with annotation 100e251 - out of range! > Warning: vertex 52329 with annotation 100e251 - out of range! > Warning: vertex 52330 with annotation 100e251 - out of range! > Warning: vertex 52331 with annotation 100e251 - out of range! > Warning: vertex 52332 with annotation 100e251 - out of range! > Warning: vertex 52333 with annotation 100e251 - out of range! > Warning: vertex 52334 with annotation 100e251 - out of range! > Warning: vertex 52335 with annotation 100e251 - out of range! > Warning: vertex 52336 with annotation 100e251 - out of range! > Warning: vertex 61927 with annotation 100e251 - out of range! > Warning: vertex 61928 with annotation 100e251 - out of range! > Warning: vertex 61929 with annotation 100e251 - out of range! > Warning: vertex 61930 with annotation 100e251 - out of range! > Warning: vertex 61931 with annotation 100e251 - out of range! > Warning: vertex 61932 with annotation 100e251 - out of range! > Warning: vertex 61933 with annotation 100e251 - out of range! > Warning: vertex 61934 with annotation 100e251 - out of range! > Warning: vertex 61935 with annotation 100e251 - out of range! > Warning: vertex 61936 with annotation 100e251 - out of range! > Warning: vertex 61937 with annotation 100e251 - out of range! > Warning: vertex 61938 with annotation 100e251 - out of range! > Warning: vertex 63766 with annotation 100e251 - out of range! > Warning: vertex 69130 with annotation 100e251 - out of range! > Warning: vertex 69131 with annotation 100e251 - out of range! > Warning: vertex 69132 with annotation 100e251 - out of range! > Warning: vertex 69133 with annotation 100e251 - out of range! > Warning: vertex 69134 with annotation 100e251 - out of range! > Warning: vertex 69135 with annotation 100e251 - out of range! > Warning: vertex 69136 with annotation 100e251 - out of range! > Warning: vertex 69137 with annotation 100e251 - out of range! > Warning: vertex 69138 with annotation 100e251 - out of range! > Warning: vertex 69139 with annotation 100e251 - out of range! > Warning: vertex 69140 with annotation 100e251 - out of range! > Warning: vertex 69141 with annotation 100e251 - out of range! > Warning: vertex 87857 with annotation 100e251 - out of range! > Warning: vertex 87858 with annotation 100e251 - out of range! > Warning: vertex 87859 with annotation 100e251 - out of range! > Warning: vertex 87860 with annotation 100e251 - out of range! > Warning: vertex 87861 with annotation 100e251 - out of range! > Warning: vertex 87865 with annotation 100e251 - out of range! > Warning: vertex 87866 with annotation 100e251 - out of range! > Warning: vertex 87867 with annotation 100e251 - out of range! > Warning: vertex 87868 with annotation 100e251 - out of range! > Warning: vertex 87869 with annotation 100e251 - out of range! > Warning: vertex 87870 with annotation 100e251 - out of range! > Warning: vertex 87871 with annotation 100e251 - out of range! > Warning: vertex 87872 with annotation 100e251 - out of range! > Warning: vertex 87873 with annotation 100e251 - out of range! > Warning: vertex 87874 with annotation 100e251 - out of range! > Warning: vertex 87875 with annotation 100e251 - out of range! > Warning: vertex 87876 with annotation 100e251 - out of range! > Warning: vertex 87877 with annotation 100e251 - out of range! > Warning: vertex 87878 with annotation 100e251 - out of range! > Warning: vertex 87879 with annotation 100e251 - out of range! > Warning: vertex 87880 with annotation 100e251 - out of range! > Warning: vertex 87881 with annotation 100e251 - out of range! > Warning: vertex 87882 with annotation 100e251 - out of range! > Warning: vertex 87883 with annotation 100e251 - out of range! > Warning: vertex 87884 with annotation 100e251 - out of range! > Warning: vertex 87885 with annotation 100e251 - out of range! > Warning: vertex 87886 with annotation 100e251 - out of range! > Warning: vertex 87887 with annotation 100e251 - out of range! > Warning: vertex 87888 with annotation 100e251 - out of range! > Warning: vertex 87889 with annotation 100e251 - out of range! > Warning: vertex 87892 with annotation 100e251 - out of range! > Warning: vertex 87893 with annotation 100e251 - out of range! > Warning: vertex 87894 with annotation 100e251 - out of range! > Warning: vertex 87896 with annotation 100e251 - out of range! > Warning: vertex 93844 with annotation 100e251 - out of range! > Warning: vertex 93846 with annotation 100e251 - out of range! > Warning: vertex 93847 with annotation 100e251 - out of range! > Warning: vertex 93848 with annotation 100e251 - out of range! > Warning: vertex 97060 with annotation 100e251 - out of range! > Warning: vertex 97061 with annotation 100e251 - out of range! > Warning: vertex 97062 with annotation 100e251 - out of range! > Warning: vertex 97063 with annotation 100e251 - out of range! > Warning: vertex 97064 with annotation 100e251 - out of range! > Warning: vertex 97065 with annotation 100e251 - out of range! > Warning: vertex 97066 with annotation 100e251 - out of range! > Warning: vertex 97067 with annotation 100e251 - out of range! > Warning: vertex 101384 with annotation 100e251 - out of range! > Warning: vertex 101385 with annotation 100e251 - out of range! > Warning: vertex 101386 with annotation 100e251 - out of range! > Warning: vertex 101387 with annotation 100e251 - out of range! > Warning: vertex 101388 with annotation 100e251 - out of range! > Warning: vertex 112617 with annotation 100e251 - out of range! > Warning: vertex 112618 with annotation 100e251 - out of range! > Warning: vertex 112619 with annotation 100e251 - out of range! > Warning: vertex 112620 with annotation 100e251 - out of range! > Warning: vertex 112623 with annotation 100e251 - out of range! > Warning: vertex 112624 with annotation 100e251 - out of range! > Warning: vertex 112625 with annotation 100e251 - out of range! > Warning: vertex 112626 with annotation 100e251 - out of range! > Warning: vertex 112627 with annotation 100e251 - out of range! > Warning: vertex 112628 with annotation 100e251 - out of range! > Warning: vertex 112629 with annotation 100e251 - out of range! > Warning: vertex 112630 with annotation 100e251 - out of range! > Warning: vertex 112631 with annotation 100e251 - out of range! > Warning: vertex 112632 with annotation 100e251 - out of range! > Warning: vertex 112633 with annotation 100e251 - out of range! > Warning: vertex 112634 with annotation 100e251 - out of range! > Warning: vertex 112635 with annotation 100e251 - out of range! > Warning: vertex 112636 with annotation 100e251 - out of range! > Warning: vertex 112637 with annotation 100e251 - out of range! > Warning: vertex 112638 with annotation 100e251 - out of range! > Warning: vertex 112639 with annotation 100e251 - out of range! > Warning: vertex 112640 with annotation 100e251 - out of range! > Warning: vertex 112641 with annotation 100e251 - out of range! > Warning: vertex 112642 with annotation 100e251 - out of range! > Warning: vertex 126633 with annotation 100e251 - out of range! > Warning: vertex 126634 with annotation 100e251 - out of range! > Warning: vertex 126635 with annotation 100e251 - out of range! > Warning: vertex 126636 with annotation 100e251 - out of range! > Warning: vertex 126637 with annotation 100e251 - out of range! > Warning: vertex 126638 with annotation 100e251 - out of range! > Warning: vertex 126639 with annotation 100e251 - out of range! > Warning: vertex 126640 with annotation 100e251 - out of range! > Warning: vertex 126641 with annotation 100e251 - out of range! > Warning: vertex 126642 with annotation 100e251 - out of range! > Warning: vertex 126643 with annotation 100e251 - out of range! > Warning: vertex 126644 with annotation 100e251 - out of range! > Warning: vertex 126645 with annotation 100e251 - out of range! > Warning: vertex 126646 with annotation 100e251 - out of range! > Warning: vertex 126647 with annotation 100e251 - out of range! > Warning: vertex 126648 with annotation 100e251 - out of range! > Warning: vertex 126649 with annotation 100e251 - out of range! > Warning: vertex 126650 with annotation 100e251 - out of range! > Warning: vertex 126651 with annotation 100e251 - out of range! > Warning: vertex 126652 with annotation 100e251 - out of range! > Warning: vertex 129154 with annotation 100e251 - out of range! > Warning: vertex 129155 with annotation 100e251 - out of range! > Warning: vertex 129156 with annotation 100e251 - out of range! > Warning: vertex 135944 with annotation 100e251 - out of range! > Warning: vertex 135945 with annotation 100e251 - out of range! > Warning: vertex 135952 with annotation 100e251 - out of range! > Warning: vertex 135953 with annotation 100e251 - out of range! > Warning: vertex 135954 with annotation 100e251 - out of range! > Warning: vertex 135955 with annotation 100e251 - out of range! > Warning: vertex 135956 with annotation 100e251 - out of range! > Warning: vertex 135957 with annotation 100e251 - out of range! > Warning: vertex 135958 with annotation 100e251 - out of range! > Warning: vertex 135959 with annotation 100e251 - out of range! > Warning: vertex 135960 with annotation 100e251 - out of range! > Warning: vertex 135961 with annotation 100e251 - out of range! > Warning: vertex 135962 with annotation 100e251 - out of range! > Warning: vertex 135963 with annotation 100e251 - out of range! > Warning: vertex 139275 with annotation 100e251 - out of range! > Warning: vertex 139276 with annotation 100e251 - out of range! > Warning: vertex 158680 with annotation 100e251 - out of range! > Warning: vertex 158681 with annotation 100e251 - out of range! > Warning: vertex 158682 with annotation 100e251 - out of range! > Warning: vertex 158683 with annotation 100e251 - out of range! > Warning: vertex 158684 with annotation 100e251 - out of range! > Warning: vertex 158685 with annotation 100e251 - out of range! > Warning: vertex 158692 with annotation 100e251 - out of range! > Warning: vertex 158693 with annotation 100e251 - out of range! > Warning: vertex 158694 with annotation 100e251 - out of range! > Warning: vertex 158695 with annotation 100e251 - out of range! > Warning: vertex 158696 with annotation 100e251 - out of range! > Warning: vertex 158697 with annotation 100e251 - out of range! > Warning: vertex 158698 with annotation 100e251 - out of range! > Warning: vertex 158699 with annotation 100e251 - out of range! > Warning: vertex 158700 with annotation 100e251 - out of range! > Warning: vertex 158701 with annotation 100e251 - out of range! > Warning: vertex 158702 with annotation 100e251 - out of range! > Warning: vertex 158703 with annotation 100e251 - out of range! > Warning: vertex 158704 with annotation 100e251 - out of range! > Warning: vertex 158705 with annotation 100e251 - out of range! > Warning: vertex 158706 with annotation 100e251 - out of range! > Warning: vertex 158707 with annotation 100e251 - out of range! > Warning: vertex 158708 with annotation 100e251 - out of range! > Warning: vertex 158709 with annotation 100e251 - out of range! > Warning: vertex 158710 with annotation 100e251 - out of range! > Warning: vertex 158711 with annotation 100e251 - out of range! > Warning: vertex 158712 with annotation 100e251 - out of range! > Warning: vertex 158713 with annotation 100e251 - out of range! > Warning: vertex 158714 with annotation 100e251 - out of range! > Warning: vertex 158715 with annotation 100e251 - out of range! > Warning: vertex 158716 with annotation 100e251 - out of range! > Warning: vertex 158717 with annotation 100e251 - out of range! > Warning: vertex 158718 with annotation 100e251 - out of range! > Warning: vertex 158722 with annotation 100e251 - out of range! > Warning: vertex 158723 with annotation 100e251 - out of range! > Warning: vertex 158724 with annotation 100e251 - out of range! > Warning: vertex 158725 with annotation 100e251 - out of range! > Warning: vertex 158726 with annotation 100e251 - out of range! > Warning: vertex 158727 with annotation 100e251 - out of range! > > _______________________________________________ > 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: 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 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.
