Hi Doug, Thank you for your reply.
This was my mris_label2annot command line: woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh --ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab --a Comp2RH_TGTN61_properGreyRH --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label --l /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label This is the terminal output: Reading ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab Number of ctab entries 76 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /home/woodward cmdline mris_label2annot --s TGT_N61AvgSubject --h rh --ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab --a Comp2RH_TGTN61_properGreyRH --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label --l /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label sysname Linux hostname Bambi machine x86_64 user woodward subject TGT_N61AvgSubject hemi rh SUBJECTS_DIR /Data/freesurfer/subjects ColorTable /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab AnnotName Comp2RH_TGTN61_properGreyRH nlables 6 LabelThresh 0 0.000000 Loading /Data/freesurfer/subjects/TGT_N61AvgSubject/surf/rh.orig 1 8355711 G_and_S_frontomargin 2 8355711 G_and_S_occipital_inf 3 8355711 G_and_S_paracentral 4 8355711 G_and_S_subcentral 5 8355711 G_and_S_transv_frontopol 6 8355711 G_and_S_cingul-Ant Mapping unhit to unknown Found 154540 unhit vertices Writing annot to /Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_properGreyRH.annot colortab file: /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab 0 Unknown 0 0 0 0 1 G_and_S_frontomargin 127 127 127 0 2 G_and_S_occipital_inf 127 127 127 0 3 G_and_S_paracentral 127 127 127 0 4 G_and_S_subcentral 127 127 127 0 5 G_and_S_transv_frontopol 127 127 127 0 6 G_and_S_cingul-Ant 127 127 127 0 7 G_and_S_cingul-Mid-Ant 127 127 127 0 8 G_and_S_cingul-Mid-Post 127 127 127 0 9 G_cingul-Post-dorsal 127 127 127 0 10 G_cingul-Post-ventral 127 127 127 0 11 G_cuneus 127 127 127 0 12 G_front_inf-Opercular 127 127 127 0 13 G_front_inf-Orbital 127 127 127 0 14 G_front_inf-Triangul 127 127 127 0 15 G_front_middle 127 127 127 0 16 G_front_sup 127 127 127 0 17 G_Ins_lg_and_S_cent_ins 127 127 127 0 18 G_insular_short 127 127 127 0 19 G_occipital_middle 127 127 127 0 20 G_occipital_sup 127 127 127 0 21 G_oc-temp_lat-fusifor 60 20 140 0 22 G_oc-temp_med-Lingual 220 180 140 0 23 G_oc-temp_med-Parahip 127 127 127 0 24 G_orbital 127 127 127 0 25 G_pariet_inf-Angular 127 127 127 0 26 G_pariet_inf-Supramar 127 127 127 0 27 G_parietal_sup 127 127 127 0 28 G_postcentral 127 127 127 0 29 G_precentral 127 127 127 0 30 G_precuneus 127 127 127 0 31 G_rectus 127 127 127 0 32 G_subcallosal 127 127 127 0 33 G_temp_sup-G_T_transv 127 127 127 0 34 G_temp_sup-Lateral 127 127 127 0 35 G_temp_sup-Plan_polar 127 127 127 0 36 G_temp_sup-Plan_tempo 127 127 127 0 37 G_temporal_inf 127 127 127 0 38 G_temporal_middle 127 127 127 0 39 Lat_Fis-ant-Horizont 127 127 127 0 40 Lat_Fis-ant-Vertical 127 127 127 0 41 Lat_Fis-post 127 127 127 0 42 Medial_wall 127 127 127 0 43 Pole_occipital 127 127 127 0 44 Pole_temporal 127 127 127 0 45 S_calcarine 127 127 127 0 46 S_central 127 127 127 0 47 S_cingul-Marginalis 127 127 127 0 48 S_circular_insula_ant 127 127 127 0 49 S_circular_insula_inf 127 127 127 0 50 S_circular_insula_sup 127 127 127 0 51 S_collat_transv_ant 100 200 200 0 52 S_collat_transv_post 127 127 127 0 53 S_front_inf 127 127 127 0 54 S_front_middle 127 127 127 0 55 S_front_sup 127 127 127 0 56 S_interm_prim-Jensen 127 127 127 0 57 S_intrapariet_and_P_trans 127 127 127 0 58 S_oc_middle_and_Lunatus 127 127 127 0 59 S_oc_sup_and_transversal 127 127 127 0 60 S_occipital_ant 61 20 180 0 61 S_oc-temp_lat 127 127 127 0 62 S_oc-temp_med_and_Lingual 141 100 220 0 63 S_orbital_lateral 127 127 127 0 64 S_orbital_med-olfact 127 127 127 0 65 S_orbital-H_Shaped 127 127 127 0 66 S_parieto_occipital 127 127 127 0 67 S_pericallosal 127 127 127 0 68 S_postcentral 127 127 127 0 69 S_precentral-inf-part 127 127 127 0 70 S_precentral-sup-part 127 127 127 0 71 S_suborbital 127 127 127 0 72 S_subparietal 127 127 127 0 73 S_temporal_inf 21 180 180 0 74 S_temporal_sup 127 127 127 0 75 S_temporal_transverse 127 127 127 0 Thanks for your help, Laura On Tue, Apr 1, 2014 at 11:40 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > What was your mris_label2annot command line? What was the terminal > output? Can you send the colortable file you passed with --ctab? > doug > > > > > On 04/01/2014 02:25 PM, Laura Taylor wrote: > > Hello, > > > > I have run mri_annotation2label and then selected the labels > > corresponding to my ROI, creating a new annotation file using > > mris_label2annot. > > > > When I load my new annotation file in freeview, the ROI's are > > displayed nicely in different colors. However the remainder of the > > brain is dark black and therefore difficult to see. > > > > I have tried to change the default color of the remainder of the brain > > to grey by editing the aparc.annot.a2009s.ctab file for my subject so > > that my ROI keep the colors originally assigned to them, but all other > > regions are changed to: > > 127 127 127 0 (grey). > > > > When I do this, my ROI's all become grey and the remainder of the > > brain stays as dark black. > > > > Can you direct me as to which file(s) I need to edit to keep my ROI's > > in color but change the remainder of the brain to a different color > > (grey). > > > > Thank you very much, > > > > Laura > > > > > > > > > > _______________________________________________ > > 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. > >
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