External Email - Use Caution

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 Caution

Dear 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

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Hsm77cRBScqDW_nMwdsLpoELTZam0Js2nL_8_Y53s2_7hJ... 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 Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1Ft5Vg1zbD9UUDeWyyHZ2LG0seV5xwReC-2x4_Ub58y8faJ0... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.