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> = ADNI = The Alzheimer's Disease Neuroimaging Initiative [[http://adni.loni.usc.edu/ | ADNI website]] [[http://www.alz.org/research/funding/partnerships/ww-adni_overview.asp | World Wide ADNI]] ---- == ADNI Data == === The most up to date complete ADNI data is here: === /autofs/space/mreuter/ADNI/download_june2014/ADNI-3T-FS-5.3-Good (cross-sectional) /autofs/space/mreuter/ADNI/download_june2014/ADNI-3T-FS-5.3-Long (longitudinal) These datasets have both been quality checked. === Longitudinal Data Information === Three stages (ADNI, ADNI-GO and ADNI2) exists with 800-1000 subjects and several time points approx. 6 months to a year apart. === Diffusion Data === /autofs/space/mreuter/ADNI/diffusion_adni2 This contains the baseline diffusion scans for ADNI2 subjects. === Manually Labeled Hippocampus Dataset === The following path leads to a dataset of 135 ADNI subjects with manually labeled hippocampus, labeled using a standard protocol. /autofs/cluster/fsm/users/samseg/subjects/ADNI135-Hippo/orig === Downloading and Processing ADNI Data === [[AdniDownloadNotes]] - For information on how to download ADNI subject data. [[AdniReconNotes]] - Recon-all notes for ADNI subjects [[AdniArchive]] - Old notes on downloading and processing the ADNI datset ---- == V6.0 Processing Update == Update as of: June 2019 The ADNI data is currently being updated to Freesurfer version 6.0 (from version 5.3). The new data is stored here: {{{/autofs/space/mreuter/ADNI/ADNI_v6.0}}}. This directory contains many sub-directories with demographics information, processed data, raw data, and any necessary scripts. The processed data directory is divided between cross-sectional and longitudinal data, and the cross-sectional section is divided between 1.5T, 3T, and the 2018_download. The 2018_download data can be moved to the appropriate magnet strength directory after processing. The raw data directory is also divided between the 1.5T, 3T, and 2018_download data. Within these directories the data is divided into multiple directories as it was downloaded in sections. The csv files in these directories contains the imageID, subjectID, age, sex, and scandate for each subject. The demographics files are described in the following demographics section. The scripts directory contains recon-commands-ADNI.csh which is the script I've been using for processing the cross-sectional data. Information on how to run the script is written at the beginning of the script. ---- == ADNI Demographics Information == The ADNI demographics information is divided between the demographics information for all ADNI data and the information we have for our downloaded data. Demographics information for all ADNI data can be found in the following directory: {{{/autofs/space/mreuter/ADNI/demographics}}} Demographics information for downloaded ADNI data can be found in the following directory: {{{/autofs/space/mreuter/ADNI/ADNI_v6.0/demographics}}} The files in these directories include: DOWNLOAD-SPECIFIC DEMOGRAPHICS ||downloaded_data_demographics.csv || contains combined demographics for downloaded imageIDs || ||field_strength_2018_download.xlsx || contains downloaded data and their field strengths|| ||Diagnosis_shortened.csv || contains imageID and diagnosis information for all ADNI data || ||ADNIMERGE_shortened.csv || shortened version of ADNIMERGE with all ADNI subjects|| MATLAB FILES (DOWNLOAD SPECIFIC ADNI DEMOGRAPHICS): ||demographics.m || Creates the downloaded_data_demographics.csv table || ||download_2018_fieldstrength.m ||Sorts data by magnet strength || ||SubjID_imageID.m || creates a txt file of the ImageIDs and SubjectIDs for the 2018 downloaded data || ALL ADNI DEMOGRAPHICS ||ADNI_demographics_final.xlsx || contains ALL demographics information connected to patient ID and image ID || ||ADNI_diagnosis.xlsx || diagnosis information for each patient ID || ||ADNIMERGE.xlsx || demographic information for each patient ID || ||ROSTER.xlsx || subject IDs and image IDs || ||ADNI_demographics_downloaded_xlsx || contains only the demographics for the ADNI files that are downloaded, also in csv format || ||converters.csv || subject IDs that converted || ||nonconverters.csv || subject IDs that did not convert || ||long.qdec.table.dat || longitudinal qdec table of ADNI demographics || ||ADNI_2018_download.csv || contains image ID, subject ID, sex, age, and acquisition date for downloaded data || MATLAB FILES (ALL ADNI DEMOGRAPHICS): ||ADNI_demographics.m || matlab file used to create ADNI_demographics_final.xlsx || ||Downloaded_demographics.m ||matlab file used to create demographics tables for only the downloaded data || ||update_download_demographics.m ||run this code with any new download to update downloaded demographics files|| ---- == ADNI Data Information == All procedures for the ADNI databases, which includes the dictionary for the abbreviations, are located here: {{{/autofs/space/mreuter/ADNI/Procedures}}} All protocols for the following data sets can be found [[http://adni.loni.usc.edu/methods/documents/ | here.]] === ANDI1 === This data set contains: * 200 normal controls * 400 MCI (mild cognitive impairment) * 200 mild AD === ADNI-GO === ADNI-GO is a follow up from ADNI1 This data set contains: * 200 EMCI (early mild cognitive impairment) * 500 normal controls and MCI from ADNI1 === ADNI2 === ADNI2 was started in 2010 and uses a different protocol than ADNI1 and ANDI-GO. This data set contains: * 150 normal controls (new) * 450-500 CN and MCI (from ADNI1) * 150 EMCI (new) * 200 EMCI (from ADNI GO) * 150 LMCI (new - late mild cognitive impairment) * 200 mild AD (new) ---- == ADNI Testing == === FreeSurfer Testing === [[ReleaseTestPlan]] - Describes the testing plan for new versions of !FreeSurfer which involves testing with the ADNI dataset. [[AdnidevtestV6]] - Notes on testing FS6.0 with the ADNI60 data. [[Buckner40Adni60Testing]] - Testing using ADNI60 === Samseg Testing === [[SamsegTesting]] - Overview of the Samseg testing, ADNI60 is used for this testing. The following links are all contain data from various Samseg testing conducted on ADNI data. [[SamsegTesting/2017-06-18]] [[SamsegTesting/2017-06-08]] [[SamsegTesting/2017-06-01_ADNI60]] [[SamsegTesting/JuneTest]] [[SamsegTesting/2017-05-26_ADNI60]] [[SamsegTesting/2017-04-14_ADNIHIPPO]] [[SamsegTesting/2017-03-06_ADNI60]] [[SamsegTesting/elastix_vs_kvlreg]] === Dementia Forecast Tool Testing === [[DementiaForecast]] - This wiki is an overview for the tool being built to predict amyloid status and forecast future clinical progression toward AD dementia. [[DementiaForecastAmyloidStatus]] [[DementiaForecastPaccPrediction]] === Other Testing with ADNI Data === [[CorticalHubs]] - Hypothesis and references for cortical hubs. [[Chubs]] - Protocol for analyzing cortical hubs (regions-of-interest defined by cortical thickness differences between older controls and individuals classified as having AD). [[SurfacePowerTest]] - Testing loss and gain of statistical power using the ADNI60 dataset. [[eTIV]] - Estimated total intracranial volume analysis, tested on ADNI datset. ---- == ADNI Related Publications == All manuscripts using ADNI data must be reviewed and approved by the ADNI Data and Publications Committee prior to submission. The DPC will strive to have a response back to you within 10 working days after you submit your manuscript so as not to slow down your efforts. Any manuscript submissions or questions may be submitted to edrake@genetics.med.harvard.edu In order to be in compliance with ADNI policies, you must include the language at the link below in the required sections (byline, title page, methods, acknowledgements) before submitting: http://adni.loni.usc.edu/wp-content/uploads/how_to_apply/ADNI_Manuscript_Citations.pdf *****ATTENTION!!!: If you have a strict page number limit like in a workshop publication, consider if you want to use ADNI data in the first place or leave at least one page free for the ADNI acknowledgements and author names.