Hi Neel,

there's not really an internal order to the annotations (they are coded by the RGB value). I would suggest posting to the afni list. Alternatively, you can use tksurfer in combo with suma to reverse engineer what they've done.

doug

Jenni Pacheco wrote:

Hi Neel,

You could refer to the surface label files that should be in your $FREESURFER_HOME directory. I believe that the $FREESURFER_HOME/Simple_surface_labels2005.txt corresponds with aparc.a2005s.annot parcellations and the $FREESURFER_HOME/average/colortable_desikan_killiany.txt corresponds with the aparc.annot parcellations.

Jenni

On Mon, 24 Jul 2006, Neel Kishan wrote:

...

Hi List,

Thanks for providing the mris_ca_label program and the two papers from 2004 and 2006. I'm using AFNI's FSread_annot to read the aparc.annot and aparc.a2005s.annot files into SUMA. The ROIs are imported numbered 0 to 34 for the aparc.annot files and 0 to 81 for the aparc.a2005s.annot files. I can see that the aparc.annot files correspond to the 2006 Desikan et al. paper, but I'm not sure how they were ordered in the annot file. I'm also wondering how the aparc.a2005s.annot files identified and ordered the ROIs.

Thanks for your help, Neel Kishan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Simple_surface_labels2005.txt was the older name. It is now called:

surface_labels.txt

and is found in $FREESURFER_HOME. Sorry!

On Mon, 2006-07-24 at 15:47 -0500, Neel Kishan wrote:

Thanks for the information. Please note that Simple_surface_labels2005.txt was not distributed in v3.0.3 for Mac OS X Tiger.

To convert an annot file to roi file for SUMA the following lines can be used for each hemisphere:

FSread_annot -input $SUBJECTS_DIR/subject/label/rh.aparc.a2005s.annot -roi_1D rh.aparc.a2005s.1D.roi FSread_annot -input $SUBJECTS_DIR/subject/label/rh.aparc.annot -roi_1D rh.aparc.1D.roi

The following list corresponds with SUMA's labeling of the first roi file: 3 G_cingulate-Isthmus 4 G_cingulate-Main_part 5 G_cuneus 6 G_frontal_inf-Opercular_part 7 G_frontal_inf-Orbital_part 8 G_frontal_inf-Triangular_part 9 G_frontal_middle 10 G_frontal_superior 11 G_frontomarginal 12 G_insular_long 13 G_insular_short 14 G_and_S_occipital_inferior 15 G_occipital_middle 16 G_occipital_superior 17 G_occipit-temp_lat-Or_fusiform 18 G_occipit-temp_med-Lingual_part 19 G_occipit-temp_med-Parahippocampal_part 20 G_orbital 21 G_paracentral 22 G_parietal_inferior-Angular_part 23 G_parietal_inferior-Supramarginal_part 24 G_parietal_superior 25 G_postcentral 26 G_precentral 27 G_precuneus 28 G_rectus 29 G_subcallosal 30 G_subcentral 31 G_temporal_inferior 32 G_temporal_middle 33 G_temp_sup-G_temp_transv_and_interm_S 34 G_temp_sup-Lateral_aspect 35 G_temp_sup-Planum_polare 36 G_temp_sup-Planum_tempolare 37 G_and_S_transverse_frontopolar 38 Lat_Fissure-ant_sgt-ramus_horizontal 39 Lat_Fissure-ant_sgt-ramus_vertical 40 Lat_Fissure-post_sgt 41 Medial_wall 42 Pole_occipital 43 Pole_temporal 44 S_calcarine 45 S_central 46 S_central_insula 47 S_cingulate-Main_part_and_Intracingulate 48 S_cingulate-Marginalis_part 49 S_circular_insula_anterior 50 S_circular_insula_inferior 51 S_circular_insula_superior 52 S_collateral_transverse_ant 53 S_collateral_transverse_post 54 S_frontal_inferior 55 S_frontal_middle 56 S_frontal_superior 57 S_frontomarginal 58 S_intermedius_primus-Jensen 59 S_intraparietal-and_Parietal_transverse 60 S_occipital_anterior 61 S_occipital_middle_and_Lunatus 62 S_occipital_superior_and_transversalis 63 S_occipito-temporal_lateral 64 S_occipito-temporal_medial_and_S_Lingual 65 S_orbital-H_shapped 66 S_orbital_lateral 67 S_orbital_medial-Or_olfactory 68 S_paracentral 69 S_parieto_occipital 70 S_pericallosal 71 S_postcentral 72 S_precentral-Inferior-part 73 S_precentral-Superior-part 74 S_subcentral_ant 75 S_subcentral_post 76 S_suborbital 77 S_subparietal 78 S_supracingulate 79 S_temporal_inferior 80 S_temporal_superior 81 S_temporal_transverse

The second file corresponds with the following list: 0 unknown/unlabeled 1 bankssts 2 caudalanteriorcingulate 3 caudalmiddlefrontal 4 corpuscallosum 5 cuneus 6 entorhinal 7 fusiform 8 inferiorparietal 9 inferiortemporal 10 isthmuscingulate 11 lateraloccipital 12 lateralorbitofrontal 13 lingual 14 medialorbitofrontal 15 middletemporal 16 parahippocampal 17 paracentral 18 parsopercularis 19 parsorbitalis 20 parstriangularis 21 pericalcarine 22 postcentral 23 posteriorcingulate 24 precentral 25 precuneus 26 rostralanteriorcingulate 27 rostralmiddlefrontal 28 superiorfrontal 29 superiorparietal 30 superiortemporal 31 supramarginal 32 frontalpole 33 temporalpole 34 transversetemporal

Jenni Pacheco wrote:

...

Hi Neel,

You could refer to the surface label files that should be in your $FREESURFER_HOME directory. I believe that the $FREESURFER_HOME/Simple_surface_labels2005.txt corresponds with aparc.a2005s.annot parcellations and the $FREESURFER_HOME/average/colortable_desikan_killiany.txt corresponds with the aparc.annot parcellations.

Jenni

On Mon, 24 Jul 2006, Neel Kishan wrote:

...

Hi List,

Thanks for providing the mris_ca_label program and the two papers from 2004 and 2006. I'm using AFNI's FSread_annot to read the aparc.annot and aparc.a2005s.annot files into SUMA. The ROIs are imported numbered 0 to 34 for the aparc.annot files and 0 to 81 for the aparc.a2005s.annot files. I can see that the aparc.annot files correspond to the 2006 Desikan et al. paper, but I'm not sure how they were ordered in the annot file. I'm also wondering how the aparc.a2005s.annot files identified and ordered the ROIs.

Thanks for your help, Neel Kishan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Neel,

the .annot files should have the color table embedded in them precisely to avoid this type of confusion. I think Doug has a tool for extracting the color table from the .annot file, don't you Doug?

cheers, Bruce

On Mon, 24 Jul 2006, Neel Kishan wrote:

surface_labels.txt has 94 ROIs in contrast to the 81 in Simple_surface_labels2005.txt, and it does not seem to match the numbering system I find in SUMA. Does this file indicate that there is another parcellating method to identify 94 ROIs?

Nick Schmansky wrote:

...

Simple_surface_labels2005.txt was the older name. It is now called:

surface_labels.txt

and is found in $FREESURFER_HOME. Sorry!

On Mon, 2006-07-24 at 15:47 -0500, Neel Kishan wrote:

...

Thanks for the information. Please note that Simple_surface_labels2005.txt was not distributed in v3.0.3 for Mac OS X Tiger.

To convert an annot file to roi file for SUMA the following lines can be used for each hemisphere:

FSread_annot -input $SUBJECTS_DIR/subject/label/rh.aparc.a2005s.annot -roi_1D rh.aparc.a2005s.1D.roi FSread_annot -input $SUBJECTS_DIR/subject/label/rh.aparc.annot -roi_1D rh.aparc.1D.roi

The following list corresponds with SUMA's labeling of the first roi file: 3 G_cingulate-Isthmus 4 G_cingulate-Main_part 5 G_cuneus 6 G_frontal_inf-Opercular_part 7 G_frontal_inf-Orbital_part 8 G_frontal_inf-Triangular_part 9 G_frontal_middle 10 G_frontal_superior 11 G_frontomarginal 12 G_insular_long 13 G_insular_short 14 G_and_S_occipital_inferior 15 G_occipital_middle 16 G_occipital_superior 17 G_occipit-temp_lat-Or_fusiform 18 G_occipit-temp_med-Lingual_part 19 G_occipit-temp_med-Parahippocampal_part 20 G_orbital 21 G_paracentral 22 G_parietal_inferior-Angular_part 23 G_parietal_inferior-Supramarginal_part 24 G_parietal_superior 25 G_postcentral 26 G_precentral 27 G_precuneus 28 G_rectus 29 G_subcallosal 30 G_subcentral 31 G_temporal_inferior 32 G_temporal_middle 33 G_temp_sup-G_temp_transv_and_interm_S 34 G_temp_sup-Lateral_aspect 35 G_temp_sup-Planum_polare 36 G_temp_sup-Planum_tempolare 37 G_and_S_transverse_frontopolar 38 Lat_Fissure-ant_sgt-ramus_horizontal 39 Lat_Fissure-ant_sgt-ramus_vertical 40 Lat_Fissure-post_sgt 41 Medial_wall 42 Pole_occipital 43 Pole_temporal 44 S_calcarine 45 S_central 46 S_central_insula 47 S_cingulate-Main_part_and_Intracingulate 48 S_cingulate-Marginalis_part 49 S_circular_insula_anterior 50 S_circular_insula_inferior 51 S_circular_insula_superior 52 S_collateral_transverse_ant 53 S_collateral_transverse_post 54 S_frontal_inferior 55 S_frontal_middle 56 S_frontal_superior 57 S_frontomarginal 58 S_intermedius_primus-Jensen 59 S_intraparietal-and_Parietal_transverse 60 S_occipital_anterior 61 S_occipital_middle_and_Lunatus 62 S_occipital_superior_and_transversalis 63 S_occipito-temporal_lateral 64 S_occipito-temporal_medial_and_S_Lingual 65 S_orbital-H_shapped 66 S_orbital_lateral 67 S_orbital_medial-Or_olfactory 68 S_paracentral 69 S_parieto_occipital 70 S_pericallosal 71 S_postcentral 72 S_precentral-Inferior-part 73 S_precentral-Superior-part 74 S_subcentral_ant 75 S_subcentral_post 76 S_suborbital 77 S_subparietal 78 S_supracingulate 79 S_temporal_inferior 80 S_temporal_superior 81 S_temporal_transverse

The second file corresponds with the following list: 0 unknown/unlabeled 1 bankssts 2 caudalanteriorcingulate 3 caudalmiddlefrontal 4 corpuscallosum 5 cuneus 6 entorhinal 7 fusiform 8 inferiorparietal 9 inferiortemporal 10 isthmuscingulate 11 lateraloccipital 12 lateralorbitofrontal 13 lingual 14 medialorbitofrontal 15 middletemporal 16 parahippocampal 17 paracentral 18 parsopercularis 19 parsorbitalis 20 parstriangularis 21 pericalcarine 22 postcentral 23 posteriorcingulate 24 precentral 25 precuneus 26 rostralanteriorcingulate 27 rostralmiddlefrontal 28 superiorfrontal 29 superiorparietal 30 superiortemporal 31 supramarginal 32 frontalpole 33 temporalpole 34 transversetemporal

Jenni Pacheco wrote:

...

Hi Neel,

You could refer to the surface label files that should be in your $FREESURFER_HOME directory. I believe that the $FREESURFER_HOME/Simple_surface_labels2005.txt corresponds with aparc.a2005s.annot parcellations and the $FREESURFER_HOME/average/colortable_desikan_killiany.txt corresponds with the aparc.annot parcellations.

Jenni

On Mon, 24 Jul 2006, Neel Kishan wrote:

...

Hi List,

Thanks for providing the mris_ca_label program and the two papers from 2004 and 2006. I'm using AFNI's FSread_annot to read the aparc.annot and aparc.a2005s.annot files into SUMA. The ROIs are imported numbered 0 to 34 for the aparc.annot files and 0 to 81 for the aparc.a2005s.annot files. I can see that the aparc.annot files correspond to the 2006 Desikan et al. paper, but I'm not sure how they were ordered in the annot file. I'm also wondering how the aparc.a2005s.annot files identified and ordered the ROIs.

Thanks for your help, Neel Kishan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer