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
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
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.eduwrote:
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 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.
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.comwrote:
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 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.
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.lab@gmail.comwrote:
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 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
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
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 <shantanu@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.lab@gmail.comwrote:
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 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
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
This is a question for Ruopeng (who is the author of freeview, and cc'ed). Can you upload the subject and the annot file so that he can replicate the problem? doug
On 04/03/2014 06:55 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.lab@gmail.com mailto: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 <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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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
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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Laura Taylor -
Shantanu Ghosh