Oy. Thanks - that worked.
On Wed, May 21, 2014 at 11:21 AM, Douglas N Greve <gr...@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 > 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. > > -- 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 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.
