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Hello,
Thank you so much for getting back to me.
This is the command that I used: mri_annotation2label --subject 01_FS --hemi lh --annotation ./01_FS/label/lh.aparc.a2009s.annot --outdir ./01_FS/label/label
This is the output when running this command:
subject = 01_FS
annotation = ./01_FS/label/lh.aparc.a2009s.annot
hemi = lh
outdir = ./01_FS/label/label
surface = white
Reading surface
/home/jingyi/MSC/FS/01_FS/surf/lh.white
Loading annotations from ./01_FS/label/lh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2009.txt)
Seg base 0
max index = 75
0 8432 ./01_FS/label/label/lh.Unknown.label
1 1395 ./01_FS/label/label/lh.G_and_S_frontomargin.label
2 1863 ./01_FS/label/label/lh.G_and_S_occipital_inf.label
3 1716 ./01_FS/label/label/lh.G_and_S_paracentral.label
4 1266 ./01_FS/label/label/lh.G_and_S_subcentral.label
5 705 ./01_FS/label/label/lh.G_and_S_transv_frontopol.label
6 2078 ./01_FS/label/label/lh.G_and_S_cingul-Ant.label
7 1282 ./01_FS/label/label/lh.G_and_S_cingul-Mid-Ant.label
8 1368 ./01_FS/label/label/lh.G_and_S_cingul-Mid-Post.label
9 541 ./01_FS/label/label/lh.G_cingul-Post-dorsal.label
10 311 ./01_FS/label/label/lh.G_cingul-Post-ventral.label
11 2286 ./01_FS/label/label/lh.G_cuneus.label
12 1098 ./01_FS/label/label/lh.G_front_inf-Opercular.label
13 404 ./01_FS/label/label/lh.G_front_inf-Orbital.label
14 1010 ./01_FS/label/label/lh.G_front_inf-Triangul.label
15 4262 ./01_FS/label/label/lh.G_front_middle.label
16 8042 ./01_FS/label/label/lh.G_front_sup.label
17 733 ./01_FS/label/label/lh.G_Ins_lg_and_S_cent_ins.label
18 745 ./01_FS/label/label/lh.G_insular_short.label
19 2056 ./01_FS/label/label/lh.G_occipital_middle.label
20 1864 ./01_FS/label/label/lh.G_occipital_sup.label
21 2682 ./01_FS/label/label/lh.G_oc-temp_lat-fusifor.label
22 3532 ./01_FS/label/label/lh.G_oc-temp_med-Lingual.label
23 1328 ./01_FS/label/label/lh.G_oc-temp_med-Parahip.label
24 2597 ./01_FS/label/label/lh.G_orbital.label
25 3531 ./01_FS/label/label/lh.G_pariet_inf-Angular.label
26 2695 ./01_FS/label/label/lh.G_pariet_inf-Supramar.label
27 4043 ./01_FS/label/label/lh.G_parietal_sup.label
28 2732 ./01_FS/label/label/lh.G_postcentral.label
29 3188 ./01_FS/label/label/lh.G_precentral.label
30 3418 ./01_FS/label/label/lh.G_precuneus.label
31 984 ./01_FS/label/label/lh.G_rectus.label
32 548 ./01_FS/label/label/lh.G_subcallosal.label
33 638 ./01_FS/label/label/lh.G_temp_sup-G_T_transv.label
34 2147 ./01_FS/label/label/lh.G_temp_sup-Lateral.label
35 642 ./01_FS/label/label/lh.G_temp_sup-Plan_polar.label
36 911 ./01_FS/label/label/lh.G_temp_sup-Plan_tempo.label
37 2662 ./01_FS/label/label/lh.G_temporal_inf.label
38 2656 ./01_FS/label/label/lh.G_temporal_middle.label
39 316 ./01_FS/label/label/lh.Lat_Fis-ant-Horizont.label
40 251 ./01_FS/label/label/lh.Lat_Fis-ant-Vertical.label
41 1056 ./01_FS/label/label/lh.Lat_Fis-post.label
42 0 empty --- skipping
43 2376 ./01_FS/label/label/lh.Pole_occipital.label
44 1572 ./01_FS/label/label/lh.Pole_temporal.label
45 2719 ./01_FS/label/label/lh.S_calcarine.label
46 3077 ./01_FS/label/label/lh.S_central.label
47 1079 ./01_FS/label/label/lh.S_cingul-Marginalis.label
48 545 ./01_FS/label/label/lh.S_circular_insula_ant.label
49 1523 ./01_FS/label/label/lh.S_circular_insula_inf.label
50 1586 ./01_FS/label/label/lh.S_circular_insula_sup.label
51 1008 ./01_FS/label/label/lh.S_collat_transv_ant.label
52 567 ./01_FS/label/label/lh.S_collat_transv_post.label
53 2010 ./01_FS/label/label/lh.S_front_inf.label
54 1590 ./01_FS/label/label/lh.S_front_middle.label
55 3393 ./01_FS/label/label/lh.S_front_sup.label
56 427 ./01_FS/label/label/lh.S_interm_prim-Jensen.label
57 4413 ./01_FS/label/label/lh.S_intrapariet_and_P_trans.label
58 1045 ./01_FS/label/label/lh.S_oc_middle_and_Lunatus.label
59 1615 ./01_FS/label/label/lh.S_oc_sup_and_transversal.label
60 679 ./01_FS/label/label/lh.S_occipital_ant.label
61 1042 ./01_FS/label/label/lh.S_oc-temp_lat.label
62 2619 ./01_FS/label/label/lh.S_oc-temp_med_and_Lingual.label
63 348 ./01_FS/label/label/lh.S_orbital_lateral.label
64 677 ./01_FS/label/label/lh.S_orbital_med-olfact.label
65 1687 ./01_FS/label/label/lh.S_orbital-H_Shaped.label
66 2160 ./01_FS/label/label/lh.S_parieto_occipital.label
67 1006 ./01_FS/label/label/lh.S_pericallosal.label
68 3493 ./01_FS/label/label/lh.S_postcentral.label
69 1993 ./01_FS/label/label/lh.S_precentral-inf-part.label
70 1476 ./01_FS/label/label/lh.S_precentral-sup-part.label
71 849 ./01_FS/label/label/lh.S_suborbital.label
72 1111 ./01_FS/label/label/lh.S_subparietal.label
73 1717 ./01_FS/label/label/lh.S_temporal_inf.label
74 6860 ./01_FS/label/label/lh.S_temporal_sup.label
75 324 ./01_FS/label/label/lh.S_temporal_transverse.label
On Mon, Oct 18, 2021 at 7:55 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send your command line, terminal output, and a list of the files that it did create?
On 10/13/2021 4:33 PM, Jingyi Wang wrote:
External Email - Use CautionDear Freesurfer experts,
I am trying to obtain parahippocampus segmentations from the "?h.aparc.a2009s.annot" file. However, after running the "mri_annotation2label" commands, I cannot find any label that belongs to the parahippocampus segmentation. Any suggestions?
Thank you in advance.
Jingyi
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