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.
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
Oy.
Thanks - that worked.
On Wed, May 21, 2014 at 11:21 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
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
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