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High-resolution imaging of the medial temporal lobe in ADNI3
High-resolution imaging of the medial temporal lobe in ADNI3
The Alzheimer's Disease Neuroimaging Initiative (ADNI) has collected thousands of oblique coronal T2-weighted MRI scans, with multiple time points per participant. This dataset is an excellent resource for testing hypotheses involving effects of Alzheimer's disease and related dementias on hippocampal subfields and MTL subregions.
This page describes how to access these scans, quality assessments (QA), and automated segmentations of MTL subregions generated using ASHS data from ADNI. These instructions assume that you have registered for access to ADNI data.
Obtaining the Imaging Data
Obtaining the Imaging Data
- Go to the ADNI data site: https://ida.loni.usc.edu/login.jsp?project=ADNI&page=HOME
- In the top menu, select Download->Image Collections
- Select the Advanced Search (Beta) tab
- In the search interface, under Image Description, enter %Hippo% then press "Search"
- You will see a list of 2200 (at the time of this writing) scans
- Press the "Select All" checkbox and "Add to Collection"
- Follow prompts to download your collection
Obtaining scan QA scores and ASHS-derived measures
Obtaining scan QA scores and ASHS-derived measures
These T2-weighted images have been examined and assigned a QA score by the ADNI researchers at the PICSL Group at the University of Pennsylvania. The scans were then processed using ASHS with the "PMC Clinical" Atlas.
- Go to the ADNI data site: https://ida.loni.usc.edu/login.jsp?project=ADNI&page=HOME
- In the top menu, select Download->Study Data
- Search for documents with "ASHS" in the title
- Please read the documentation in "ASHS volume data methods (PDF)"
- The QA scores and volume measurements are in the spreadsheet "ASHS volume data [ADNI1,GO,2,3]"
- The spreadsheet "ASHS volume data Dictionary [ADNI1,GO,2,3]" contains additional metadata about itemized fields in the main spreadsheet
- Using the QA scores:
- QA scores are in columns "T2_QC_R, T2_QC_L" (separate for left/right MTL)
- Scores are from 0 (worst) to 4 (best). Images with quality 0 or 1 should not be used.
- Using the ASHS quantitative results:
- Columns "RIGHT_XXX_VOL" and "LEFT_XXX_VOL" give ASHS-derived MTL subregional volumes
- Columns "RIGHT_XXX_NS" and "LEFT_XXX_NS" give the number of slices occupied by the MTL subregions
- We recommend to normalize the volume of extrahippocampal structures (ERC, BA35, BA36, PHC) by the number of slices, as in the ASHS 2014 HBM paper.
- We also recommend reading the general "ADNI3 MRI ANALYSIS MANUAL (PDF)" document
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