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> 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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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