This is a question for Ruopeng (who is the author of freeview, and cc'ed). Can you upload the subject and the annot file so that he can replicate the problem? doug
On 04/03/2014 06:55 PM, Laura Taylor wrote: > Hi Again Doug, > > I was able to get what I was looking for after I modified my ctab file > slightly and used tksurfer instead of freeview to display the images. > I am hoping, however, that it is still possible to get things to work > in freeview. > > For the ctab file, I put my 6 parcellated ROI's at the start of the > ctab file and numbered them 1 to 6. I numbered the remaining regions > 7-75. > > In freeview the ROI's were in color but the remainder of the brain was > black (not what I wanted). However in tksurfer, everything looked > good (brain in grey and ROI's in different colors). > > Do you think it would be possible to display these images properly in > freeview as well? > > Thank you very much for your time, > > Laura > > > On Wed, Apr 2, 2014 at 10:05 AM, Laura Taylor > <taylor.cnos....@gmail.com <mailto:taylor.cnos....@gmail.com>> wrote: > > 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 <mailto: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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <mailto: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. > > > > > > _______________________________________________ > 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
