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/
> _______________________________________________
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> >>> 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
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>
>
> --
> 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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