Hi Shantanu, Thanks for your reply. My command line in tksurfer was:
~$ tksurfer TGT_N61AvgSubject rh inflated -annotation /Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_Apr3.annot You can also do the same for the pial surface. The original ctab file (r/lh.aparc.a2009s.ctab - or whichever one corresponds to the parcellation scheme that you are using) is automatically created in the labels folder for each subject (and it should be the same for each subject). I did indeed edit the ctab file using RGB color codes. I used 127 127 127 for grey for the remainder of my brain. Best wishes, Laura On Thu, Apr 3, 2014 at 5:53 PM, Shantanu Ghosh <shant...@nmr.mgh.harvard.edu > wrote: > Hi Laura, > I am facing the same problem when using freeview. Can you tell me what was > your commandline that solved the problem in tksurfer? How did you get the > ctab file and did you edit it using the RGB color codes? > Thanks in advance. > Shantanu > > > On Thu, April 3, 2014 6:55 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>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> 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. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > -- > Not only is the universe stranger than we think, it is stranger than we > can think. -Werner Heisenberg > > > >
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