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= ADNI Download Notes = |
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| cd /autofs/cluster/con_002/users/ADNI | cd /autofs/space/mreuter/ADNI |
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| It is necessary to obtain an account with them in order to download data from the LONI site, which is here: | It is necessary to obtain an account with them in order to download data from the LONI site, which is here: |
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| === T2/PD data === * on the LONI ADNI page, click on Search->Advanced Search * for 'month 0' scans, select both Screening and Baseline, or select one of the other months (for longitudinal scans) * enter '*PD*T2*' in the MRI Series Description text box * select PD and T2 weighting * select Image count All * click the SEARCH button * now you will need to save the matches, to do this you will need to select each scan on every page of the results (there could be 20 or more pages of results, because the stupid interface seems to display only 20 at a time). click the 'Click here to select all series on the page' checkbox, but then uncheck duplicate scans for the same subject. * before going to the next page, click Add to Collection. if this is the first page of the search, then create a new collection name (say, 'Month_6_PDT2'). Click Add. * repeat the 'select all', 'unselect duplicates', 'add to collection' step for each page of the search results (warning! this is mind numbingly boring, tedious and time consuming!) * once the image collection is done, click on Download->Image Collections, in My Collections, find the collection you just created and select 'not downloaded' * select the 'All' checkbox * select the 'Nifti' radio button * click DOWNLOAD, this brings-up a java box which then prompts for a directory. once that is selected, then it will being downloading, which could take days.... * now for the fun part... |
'''Previous Download Date: 6/25/18''' ---- == Steps for Downloading Data == |
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| * Go the the following website to access the data: http://adni.loni.usc.edu/data-samples/access-data/ * If you do not have an account, you can apply for access here: https://ida.loni.usc.edu/collaboration/access/appLicense.jsp NOTE: It takes approximately 2-3 weeks to gain access to the data * Once you are logged into the website, on the top bar select Download -> Image Collections. {{attachment:ADNI_imageCollection.png}} * Once on the Image Collections page, select Advanced Search. This will bring you to the location where you can select parameters for the data you wish to download. {{attachment:ADNI_advancedDownload.png}} * On the Advanced Search tab, there a few parameters that were previously used to download the data. First, for the Study Date, click the dropdown and change it to "Between", then enter the date of the previous data download in the start date, and the current date in the end date. Make sure to record the current date so we know for future downloads. Next, for the Image Description, you will need to search twice using different criteria for this field. Search once using “N3m” and again using “scaled”. Finally, under Image Protocol -> Weighting, check the box next to "T1". {{attachment:ADNI_advancedDownload2.png}} * Once the search results load, select the scans you wish to download and add them to a new image collection. * After you have all the scans in the image collection, download the csv file associated with the image collection. This file is important because it contains information regarding the image ID, subject ID, group, age, and more. * Finally, select the images from the collection you wish to download and click the "1-Click Download" option. NOTE: this can take several hours or several days to download depending on the number of files. |
See also AdniReconNotes
ADNI Download Notes
Notes on how to download ADNI subject data and incorporate into our local copy, which is found here:
cd /autofs/space/mreuter/ADNI
The main ADNI site is here: http://adni.loni.ucla.edu/
It is necessary to obtain an account with them in order to download data from the LONI site, which is here: https://ida.loni.ucla.edu/login.jsp?project=ADNI
Previous Download Date: 6/25/18
Steps for Downloading Data
Go the the following website to access the data: http://adni.loni.usc.edu/data-samples/access-data/
If you do not have an account, you can apply for access here: https://ida.loni.usc.edu/collaboration/access/appLicense.jsp
- NOTE: It takes approximately 2-3 weeks to gain access to the data
Once you are logged into the website, on the top bar select Download -> Image Collections.
- Once on the Image Collections page, select Advanced Search. This will bring you to the location where you can select parameters for the data you wish to download.
On the Advanced Search tab, there a few parameters that were previously used to download the data. First, for the Study Date, click the dropdown and change it to "Between", then enter the date of the previous data download in the start date, and the current date in the end date. Make sure to record the current date so we know for future downloads. Next, for the Image Description, you will need to search twice using different criteria for this field. Search once using “N3m” and again using “scaled”. Finally, under Image Protocol -> Weighting, check the box next to "T1".
- Once the search results load, select the scans you wish to download and add them to a new image collection.
- After you have all the scans in the image collection, download the csv file associated with the image collection. This file is important because it contains information regarding the image ID, subject ID, group, age, and more.
- Finally, select the images from the collection you wish to download and click the "1-Click Download" option. NOTE: this can take several hours or several days to download depending on the number of files.