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LCN Cortical Lobes Dataset
The LCN-CortLobes dataset is a collection of manually-inspected cortical lobe labels created from FreeSurfer-processing the T1w MR images of 35 subjects, ages 64 - 96, originating from the ADNI and OASIS datasets. The set is intended to supplement the Mindboggle-101 dataset of cortical labels Klien and Tourville, 2012, which lack image data of subjects over the age of 61, and lack image data acquired on GE scanners. Unlike the Mindboggle set, only the cortical lobes (frontal, parietal, temporal and occipital) have been manually inspected. The lobe labels are composed from the freesurfer-generated cortical regions, following the DKT labeling protocol, as described in the appendix of the Klein and Tourville paper. The DKT cortical regions in the LCN-CortLobes dataset have not been manually inspected.
The set is freely available for download (see Data Download below).
Methods
Data
To address two shortcomings in the Mindboggle dataset, images from publicly available datasets were identified following this criteria:
- subjects over the age of 61
- subjects scanned on GE MRI scanners
34 subjects were identified in the ADNI dataset, and 1 subject from the OASIS. The selected T1-weighted images were free of image artifacts. The demographic and scanner information is shown in the table below (included in the dataset distribution). Note that several subjects were diagnosed with Alzheimer's Disease (AD), mild cognitive impairment (MCI), and late-stage MCI (LMCI). The remaining were cognitively normal (CN).
subject_id |
age |
sex |
manufacturer |
field_strength |
diagnosis |
source |
002_S_0295_13722 |
84.9041 |
M |
GE |
1.5 |
CN |
ADNI |
002_S_0413_14437 |
76.3863 |
F |
GE |
1.5 |
CN |
ADNI |
002_S_0685_18211 |
89.737 |
F |
GE |
1.5 |
CN |
ADNI |
002_S_0685_MR1 |
93 |
F |
GE |
1.5 |
CN |
ADNI |
002_S_0782_20519 |
81.7068 |
M |
GE |
1.5 |
MCI |
ADNI |
002_S_0816_49010 |
71.4849 |
M |
GE |
1.5 |
AD |
ADNI |
002_S_0954_108600 |
71.0795 |
F |
GE |
1.5 |
MCI |
ADNI |
003_S_0907_MR1 |
95 |
F |
Siemens |
1.5 |
CN |
ADNI |
003_S_1074_MR1 |
91 |
F |
Siemens |
1.5 |
MCI |
ADNI |
005_S_0221_11604 |
67.5315 |
M |
GE |
1.5 |
AD |
ADNI |
005_S_0222_11299 |
85.9918 |
M |
GE |
1.5 |
MCI |
ADNI |
005_S_0602_66117 |
72.0685 |
M |
GE |
3 |
CN |
ADNI |
005_S_1341_43188 |
71.6521 |
F |
GE |
1.5 |
AD |
ADNI |
006_S_0322_17197 |
65.6658 |
M |
GE |
1.5 |
MCI |
ADNI |
006_S_6441_MR1 |
89 |
M |
Philips |
3 |
MCI |
ADNI |
007_S_0101_9602 |
73.6712 |
M |
GE |
1.5 |
LMCI |
ADNI |
007_S_0128_10007 |
64.1699 |
F |
GE |
1.5 |
MCI |
ADNI |
009_S_0842_24339 |
73.7315 |
M |
GE |
1.5 |
CN |
ADNI |
009_S_0862_25128 |
73.5041 |
F |
GE |
1.5 |
CN |
ADNI |
009_S_1030_28514 |
67.5507 |
M |
GE |
1.5 |
LMCI |
ADNI |
029_S_1073_30359 |
65.7699 |
F |
GE |
1.5 |
MCI |
ADNI |
032_S_6293_MR1 |
88 |
F |
Siemens |
3 |
CN |
ADNI |
094_S_1293_98699 |
78.2466 |
M |
GE |
3 |
MCI |
ADNI |
098_S_0172_11398 |
70.6904 |
F |
GE |
1.5 |
CN |
ADNI |
126_S_0606_37834 |
69.1397 |
F |
GE |
3 |
AD |
ADNI |
126_S_0784_25775 |
76.0055 |
F |
GE |
1.5 |
AD |
ADNI |
127_S_0259_11888 |
70.663 |
M |
GE |
1.5 |
CN |
ADNI |
127_S_0260_28530 |
79.3945 |
F |
GE |
3 |
CN |
ADNI |
127_S_0393_30421 |
86.8466 |
F |
GE |
3 |
MCI |
ADNI |
127_S_0754_23787 |
67.7178 |
F |
GE |
1.5 |
AD |
ADNI |
127_S_0844_29229 |
85.4603 |
F |
GE |
3 |
AD |
ADNI |
131_S_0384_14252 |
79.9616 |
M |
GE |
3 |
LMCI |
ADNI |
131_S_1389_78461 |
76.8192 |
M |
GE |
3 |
LMCI |
ADNI |
133_S_0525_16133 |
70.1425 |
F |
GE |
1.5 |
CN |
ADNI |
OAS1_0278_MR1 |
96 |
F |
Siemens |
1.5 |
HC |
OASIS |
Processing
The standard processing stream ("recon-all -all") of FreeSurfer v7.0.0 was used to create subcortical and cortical segmentations and parcellations. All images completed processing without errors. FreeSurfer automatically creates cortical parcellation following the DKT labeling protocol (described in the appendix of the Klein and Tourville paper). The FreeSurfer utility "mri_annotation2label --lobesStrict ?h.DKTlobes.annot --annotation ?h.aparc.DKTatlas.annot" was used to create the cortical lobe surface labels (?h.DKTlobes.annot).
Inspection
Bruce Fischl, Ph.D., Professor in Radiology at Harvard Medical School, Neuroscientist at Massachusetts General Hospital, conducted a visual inspection of image snapshots of the cortical lobe labels. For each subject, and for each hemisphere, a snapshot of the lateral and medial surfaces, both the 'pial' and 'inflated' surfaces, were generated by the FreeSurfer utility "freeview". An example of the set of snapshots generated for each subject is shown below:
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Results
Data Download
The set includes the following files:
- demographics.tsv - spreadsheet of info on the set's 35 subjects:
- subject_id
- age (64 - 96)
- sex (M or F)
- manufacturer (GE, Siemens or Philips)
- field_strength (1.5 or 3)
- diagnosis (CN = cognitively normal, MCI = mild cognitive impairment, LMCI = late-stage MCI, AD = Alzheimer's Disease)
- source (ADNI or OASIS)
<subject_id>/mri - folder containing:
- orig.mgz - the T1w input
- aseg.DKTatlas+aseg.mgz - the labeled volume of DKT cortical regions and subcortical structure segmentations (note: not an inspected file)
- aseg.DKTlobes+aseg.mgz - the labeled volume of cortical lobes and subcortical structure segmentations (note: not an inspected file)
<subject_id>/label - folder containing:
?h.DKTlobes.annot - the surface labels for the cortical lobes, created from mri_annotation2label --lobesStrict, manually inspected
- ?h.aparc.DKTatlas.annot - the surface labels for the DKT cortical regions (note: not manually inspected)
- lobesQA - folder containing snapshots taken of the cortical surface showing the lobes, used in the manual inspection process
Conflict of Interest Statement