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
greve@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/

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