Re: Re: [Freesurfer] Parcellation data order - Freesurfer

21 Aug 2006


      Hi Feng,
there's an update matlab reader that also extracts the color table, 
contributed by Thomas Yeo. I've attached it if you're interested.
cheers,
Bruce
On Mon, 21 Aug 2006, fshi wrote:
...
Hi Dr. Bruce Fischl,
I subscribe this mailing list form july. I'm glad to answer some questions if I know.
I think I find the way how color table correspond to the big numbers in annot files.
Just translate the three color values from decimal to binary like 00001111, and put them
together, and then translate the number back to decimal, now you can get the numbers read
form annot files.
The correspondance between color table and numbers in annot files:
(for example: 1	G_cingularis	25	60	60				3947545)
comments:    ~~~index           ~~~~~~~~~~RGB color     ~~~~~~~numbers computed by color
                                                       used in annot files instead of color
0	Unknown	0	0	0	0
1	G_cingularis	25	60	60	3947545
2	G_cuneus	180	20	20	1316020
3	G_frontalis_inf-pars_opercularis	220	20	100	6558940
4	G_frontalis_inf-pars_orbitalis	140	60	60	3947660
5	G_frontalis_inf-pars_triangularis	180	220	140	9231540
6	G_frontalis_medius	140	100	180	11822220
7	G_frontalis_sup-pars_lateralis	180	20	140	9180340
8	G_frontalis_sup-pars_medialis	180	140	100	6589620
9	G_frontomarginalis	140	20	140	9180300
10	G_hippocampi	25	180	20	1356825
11	G_insularis_breves	225	140	140	9211105
12	G_occipitalis_inf	140	220	100	6610060
13	G_occipitalis_medius-pars_inf	180	60	180	11812020
14	G_occipitalis_medius-pars_sup	180	60	180	11812020
15	G_occipitalis_sup	20	220	60	3988500
16	G_lateralis	60	20	140	9180220
17	G_lingualis	220	180	140	9221340
18	G_parahippocampi	65	100	20	1336385
19	G_orbitalis	220	60	20	1326300
20	G_paracentralis	60	100	60	3957820
21	G_parietalis_inf-pars_angularis	20	60	220	14433300
22	G_parietalis_inf-pars_supramarginalis	100	100	60	3957860
23	G_parietalis_sup	220	180	220	14464220
24	G_postcentralis	20	180	140	9221140
25	G_precentralis	60	140	180	11832380
26	G_precuneus	25	20	140	9180185
27	G_rectus_and_S_orbitalis_medialis	20	60	100	6568980
28	G_rectus_and_S_orbitalis_medialis2	20	60	100	6568980
29	G_subcentralis	60	20	220	14423100
30	G_supracingularis	145	220	220	14474385
31	G_temporalis_transversalis	225	60	60	3947745
32	G_temporalis_inf	220	220	100	6610140
33	G_temporalis_medius	180	60	60	3947700
34	G_temporalis_sup-pars_lateralis	220	60	220	14433500
35	G_temporalis_sup-planum_polare	60	220	60	3988540
36	G_temporalis_sup-planum_temporale	20	140	20	1346580
37	Plica_falciformis	141	220	100	6610061
38	Polus_occipitalis	140	20	60	3937420
39	Polus_temporalis	220	180	20	1357020
40	S_temporalis_transversalis	221	60	60	3947741
42	S_angularis	181	20	20	1316021
43	S_calcarinus	61	180	180	11842621
44	S_centralis_insulae_&_G_insularis_longus	21	220	20	1367061
46	S_centralis	221	20	20	1316061
47	S_cingularis	181	100	20	1336501
48	S_cingularis-pars_marginalis	221	20	100	6558941
49	S_circularis_insulae_ant	221	60	140	9190621
50	S_circularis_insulae_inf	221	20	220	14423261
51	S_circularis_insulae_sup	61	220	220	14474301
52	S_corpori_callosi	181	220	20	1367221
53	S_diagonalis	21	60	20	1326101
54	S_frontalis_inf	221	220	20	1367261
55	S_frontalis_medialis	141	60	60	3947661
56	S_frontalis_medius	141	20	100	6558861
57	S_frontalis_sup	61	220	100	6609981
58	S_frontomarginalis	21	220	60	3988501
59	S_intermedius_primus	141	60	20	1326221
60	S_intermedius_secundus	141	100	100	6579341
61	S_intracingularis	181	60	20	1326261
62	S_intraoccipitalis_medius	141	140	20	1346701
63	S_intraoccipitotemporalis_lateralis	221	180	180	11842781
64	S_intraparietalis	141	20	220	14423181
65	S_lateralis-pars_ant-ramus_horizontalis	61	20	220	14423101
66	S_lateralis-pars_ant-ramus_verticalis	61	20	60	3937341
67	S_lateralis-pars_horizontalis	101	100	220	14443621
68	S_lateralis-pars_post	61	60	100	6569021
69	S_lunatus	141	180	100	6599821
70	S_occipitalis_ant	61	20	180	11801661
71	S_occipitalis_inf	21	60	180	11811861
72	S_occipitalis_medius	101	60	220	14433381
73	S_occipitalis_sup	21	20	140	9180181
74	S_occipitalis_transversalis	61	20	20	1315901
75	S_occipitopolaris	201	240	60	3993801
76	S_occipitotemporalis_lateralis	221	140	20	1346781
77	S_occipitotemporalis_medialis	141	100	220	14443661
78	S_orbitales	101	20	20	1315941
79	S_orbitalis_lateralis	221	100	20	1336541
80	S_paracalcarinus	221	140	100	6589661
81	S_paracentralis	21	180	140	9221141
82	S_parietalis_transversalis	181	100	60	3957941
83	S_parieto_occipitalis	101	100	180	11822181
84	S_postcentralis	21	140	220	14453781
85	S_precentralis	21	20	220	14423061
86	S_retrocalcarinus	21	100	20	1336341
87	S_rhinalis	221	100	100	6579421
88	S_subcentralis_ant_&_post_	61	180	60	3978301
89	S_suborbitalis	21	20	60	3937301
90	S_subparietalis	101	60	60	3947621
91	S_supracingularis	21	220	220	14474261
92	S_temporalis_inf	21	180	180	11842581
93	S_temporalis_sup	221	220	60	3988701
94	S_triangularis	181	140	140	9211061
The way read annot files with matlab (taken from archives of this maillist)
function [annots] = read_annotation(fname)
%
% [annots] = read_annotation(fname)
% reads a binary annotation file into a vector
%
% open it as a big-endian file
fid = fopen(fname, 'rb', 'b') ;
if (fid < 0)
    str = sprintf('could not open annotation file %s.', fname) ;
    error(str) ;
end
vnum = fread(fid, 1, 'int32') ;
tmp = fread(fid, vnum*2, 'int') ;
annots = tmp(2:2:vnum*2) ;
fclose(fid) ;
   Hope it useful.


Feng Shi,
Automation Institute,Chinese Academy of Sciences,Beijing,China
======= 2006-07-25 09:13:28 =======
...
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
>
>
>
>

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Feng Shi, Ph.D. Candidate
Medical Imaging and Computing Group
National Laboratory of Pattern Rcognition
Automation Institute,Chinese Academy of Sciences
Beijing, 100080
+86-10-62659278(Office)
fshi@nlpr.ia.ac.cn