Your color table appears to have been created in windows (or maybe mac). Convert it to a unix text file. doug
On 05/21/2014 10:40 AM, Paul Beach wrote: > Freesurfer folks, > > I'm trying to compile an annotation using mris_label2annot after > transferring fsaverage5 labels to a single subject. I'm getting a > strange error. Essentially it looks like it can't find most of my > transferred labels, which doesn't make sense as they are definitely in > the directory in which I'm executing the command. The same error > happens with both hemispheres. I am including an 'unknown' entry in > the ctab files. I've tried changing things around with my ctab files > and it looks like it just won't take in anything past the first '-l' > flag in the mris_label2annot command. > /Reading ctab rh.Yeo_7Net_split.ctab/ > /Number of ctab entries 2/ > / > / > /$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $/ > /cwd > /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/ > /cmdline mris_label2annot --s HS_001 --h rh --ctab > rh.Yeo_7Net_split.ctab --annot Yeo_7Net_split_aparc --l > rh.Background+FreeSurfer_Defined_Medial_Wall.label --l > rh.7Networks_RH_Vis.label --l rh.7Networks_RH_SomMot.label --l > rh.7Networks_RH_DorsAttn_Post.label --l > rh.7Networks_RH_DorsAttn_FEF.label --l > rh.7Networks_RH_DorsAttn_PrCv.label --l > rh.7Networks_RH_SalVentAttn_TempOccPar.label --l > rh.7Networks_RH_SalVentAttn_PrC.label --l > rh.7Networks_RH_SalVentAttn_FrOper.label --l > rh.7Networks_RH_SalVentAttn_PFCv.label --l > rh.7Networks_RH_SalVentAttn_PFCl.label --l > rh.7Networks_RH_SalVentAttn_Med.label --l > rh.7Networks_RH_Limbic_OFC.label --l > rh.7Networks_RH_Limbic_TempPole.label --l > rh.7Networks_RH_Cont_Par.label --l rh.7Networks_RH_Cont_Temp.label --l > rh.7Networks_RH_Cont_PFCv.label --l rh.7Networks_RH_Cont_PFCl.label > --l rh.7Networks_RH_Cont_pCun.label --l > rh.7Networks_RH_Cont_Cing.label --l rh.7Networks_RH_Cont_PFCmp.label > --l rh.7Networks_RH_Default_Par.label --l > rh.7Networks_RH_Default_Temp.label --l > rh.7Networks_RH_Default_PFCv.label --l > rh.7Networks_RH_Default_PFCm.label --l rh.7Networks_RH_Default_PCC.label / > /sysname Linux/ > /hostname gauss.rad.msu.edu <http://gauss.rad.msu.edu>/ > /machine x86_64/ > /user beachpau/ > / > / > /subject HS_001/ > /hemi rh/ > /SUBJECTS_DIR /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/ > /ColorTable rh.Yeo_7Net_split.ctab/ > /AnnotName Yeo_7Net_split_aparc/ > /nlables 26/ > /LabelThresh 0 0.000000/ > /Loading > /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/surf/rh.orig/ > / 1 65793 rh.Background+FreeSurfer_Defined_Medial_Wall/ > / 2 -1 NOT_FOUND/ > / 3 -1 NOT_FOUND/ > / 4 -1 NOT_FOUND/ > / 5 -1 NOT_FOUND/ > / 6 -1 NOT_FOUND/ > / 7 -1 NOT_FOUND/ > / 8 -1 NOT_FOUND/ > / 9 -1 NOT_FOUND/ > /10 -1 NOT_FOUND/ > /11 -1 NOT_FOUND/ > /12 -1 NOT_FOUND/ > /13 -1 NOT_FOUND/ > /14 -1 NOT_FOUND/ > /15 -1 NOT_FOUND/ > /16 -1 NOT_FOUND/ > /17 -1 NOT_FOUND/ > /18 -1 NOT_FOUND/ > /19 -1 NOT_FOUND/ > /20 -1 NOT_FOUND/ > /21 -1 NOT_FOUND/ > /22 -1 NOT_FOUND/ > /23 -1 NOT_FOUND/ > /24 -1 NOT_FOUND/ > /25 -1 NOT_FOUND/ > /26 -1 NOT_FOUND/ > /Mapping unhit to unknown/ > /Found 5 unhit vertices/ > /Writing annot to > /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/HS_001/label/rh.Yeo_7Net_split_aparc.annot/ > > I have attached my .ctab files in case they would help. > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) > > > _______________________________________________ > 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 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.
