Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

Try excluding the following line from your ctab

0 Unknown 0 0 0 0

The list in the ctab should match that of the labels you are passing on the command line (it is ok to have more in the ctab than on the command line)

doug

On 04/02/2014 01:05 PM, Laura Taylor 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 <greve@nmr.mgh.harvard.edu mailto:greve@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
>
>
>
>
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