Summary of what happened:
The correspondence of CAB-NP ROI numbers to grayordinate indices is unclear in my coding.
(Now, about only surface is all to know; CAB-NP 1~360)
To know that, I got CAB-NP label files from
- ColeAnticevicNetPartition/CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_ReorderedByNetworks.dscalar.nii at master · ColeLab/ColeAnticevicNetPartition · GitHub
- ColeAnticevicNetPartition/Glasser360Indices_LR.dscalar.nii at master · ColeLab/ColeAnticevicNetPartition · GitHub
- ColeAnticevicNetPartition/CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_ReorderedByNetworks.dlabel.nii at master · ColeLab/ColeAnticevicNetPartition · GitHub
and visualized labels, but it doesn’t seems to assigned with grayordinate numbers as below.
How should we get the correct assignments ?
Command used (and if a helper script was used, a link to the helper script or the command generated):
import numpy as np
import nibabel as nib
label = np.squeeze(nib.load('CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_ReorderedByNetworks.dlabel.nii').get_fdata()).astype(int)
print(label[:100])
# output
548 162 362 364 76 418 408 89 415 169 571 547 547 547 547 399 399 399
399 399 547 547 547 547 547 547 547 547 546 546 546 546 546 546 546 544
544 544 544 544 544 544 544 544 544 544 544 2 2 2 2 2 2 1
1 1 1 1 1 1 1 1 1 1 72 72 72 72 72 89 89 89
89 89 89 89 568 568 568 567 567 567 567 569 569 569 569 569 569 89
89 89 89 89 547 547 547 399 399 399
label = np.squeeze(nib.load('Glasser360Indices_LR.dscalar.nii').get_fdata()).astype(int)
print(label[:100])
# output
35 52 12 26 13 149 85 153 133 102 131 34 34 34 34 14 14 14
14 14 34 34 34 34 34 34 34 34 33 33 33 33 33 33 33 31
31 31 31 31 31 31 31 31 31 31 31 121 121 121 121 121 121 1
1 1 1 1 1 1 1 1 1 1 4 4 4 4 4 153 153 153
153 153 153 153 120 120 120 119 119 119 119 126 126 126 126 126 126 153
153 153 153 153 34 34 34 14 14 14
label = np.squeeze(nib.load('CortexSubcortex_ColeAnticevic_NetPartition_wSubcorGSR_parcels_LR_ReorderedByNetworks.dscalar.nii').get_fdata()).astype(int)
print(label[:100])
# output
548 162 362 364 76 418 408 89 415 169 571 547 547 547 547 399 399 399
399 399 547 547 547 547 547 547 547 547 546 546 546 546 546 546 546 544
544 544 544 544 544 544 544 544 544 544 544 2 2 2 2 2 2 1
1 1 1 1 1 1 1 1 1 1 72 72 72 72 72 89 89 89
89 89 89 89 568 568 568 567 567 567 567 569 569 569 569 569 569 89
89 89 89 89 547 547 547 399 399 399
Environment (Docker, Singularity / Apptainer, custom installation):
python 3.13.2
numpy 2.1.3
nibabel 5.3.2