rmarkello / abagen

A toolbox for working with Allen Human Brain Atlas microarray expression data
https://abagen.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Issue with relabel_gifti? #200

Open ik362 opened 3 years ago

ik362 commented 3 years ago

Hi there, Great package thanks for sharing!

I am trying to use the relabel_gifti function however I keep running into a small issue. For context: I am trying to get gene expression for Destrieux Atlas ROIs.

First I convert annot files to gifti:

destrieuxLeftTemp = abagen.annot_to_gifti('/home/nilearn_data/destrieux_surface/left.aparc.a2009s.annot')
destrieuxRightTemp = abagen.annot_to_gifti('/home/nilearn_data/destrieux_surface/right.aparc.a2009s.annot')

Then I relabel:

destrieuxLeft, destrieuxRight = relabel_gifti((destrieuxLeftTemp, destrieuxRightTemp), background=['Unknown'], offset=76)

However, when I look at the label tables the last label is not reannotated:


print(destrieuxRight.labeltable.print_summary())

{0: 'Unknown', 78: 'G_and_S_frontomargin', 79: 'G_and_S_occipital_inf', 80: 'G_and_S_paracentral',
81: 'G_and_S_subcentral', 82: 'G_and_S_transv_frontopol', 83: 'G_and_S_cingul-Ant', 84: 'G_and_S_cingul-Mid-Ant',
85: 'G_and_S_cingul-Mid-Post', 86: 'G_cingul-Post-dorsal', 87: 'G_cingul-Post-ventral', 88: 'G_cuneus',
89: 'G_front_inf-Opercular', 90: 'G_front_inf-Orbital', 91: 'G_front_inf-Triangul', 92: 'G_front_middle', 93: 'G_front_sup',
94: 'G_Ins_lg_and_S_cent_ins', 95: 'G_insular_short', 96: 'G_occipital_middle', 97: 'G_occipital_sup',
98: 'G_oc-temp_lat-fusifor', 99: 'G_oc-temp_med-Lingual', 100: 'G_oc-temp_med-Parahip', 101: 'G_orbital',
102: 'G_pariet_inf-Angular', 103: 'G_pariet_inf-Supramar', 104: 'G_parietal_sup', 105: 'G_postcentral', 106: 'G_precentral',
107: 'G_precuneus', 108: 'G_rectus', 109: 'G_subcallosal', 110: 'G_temp_sup-G_T_transv', 111: 'G_temp_sup-Lateral',
112: 'G_temp_sup-Plan_polar', 113: 'G_temp_sup-Plan_tempo', 114: 'G_temporal_inf', 115: 'G_temporal_middle',
116: 'Lat_Fis-ant-Horizont', 117: 'Lat_Fis-ant-Vertical', 118: 'Lat_Fis-post', 119: 'Medial_wall', 120: 'Pole_occipital',
121: 'Pole_temporal', 122: 'S_calcarine', 123: 'S_central', 124: 'S_cingul-Marginalis', 125: 'S_circular_insula_ant',
126: 'S_circular_insula_inf', 127: 'S_circular_insula_sup', 128: 'S_collat_transv_ant', 129: 'S_collat_transv_post',
130: 'S_front_inf', 131: 'S_front_middle', 132: 'S_front_sup', 133: 'S_interm_prim-Jensen',
134: 'S_intrapariet_and_P_trans', 135: 'S_oc_middle_and_Lunatus', 136: 'S_oc_sup_and_transversal',
137: 'S_occipital_ant', 138: 'S_oc-temp_lat', 139: 'S_oc-temp_med_and_Lingual', 140: 'S_orbital_lateral',
141: 'S_orbital_med-olfact', 142: 'S_orbital-H_Shaped', 143: 'S_parieto_occipital', 144: 'S_pericallosal',
145: 'S_postcentral', 146: 'S_precentral-inf-part', 147: 'S_precentral-sup-part', 148: 'S_suborbital',
149: 'S_subparietal', 150: 'S_temporal_inf', 151: 'S_temporal_sup', 75: 'S_temporal_transverse'}
None

The key of the last entry remains 75 after the relabel but as far a ! can tell it should be 152. Is there anyway to change the value of this entry?

Thanks for your help!