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.lab@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 <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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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