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
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