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NA-MIC Driving Biological Projects investigators have made several datasets available to NA-MIC developers. This page provides information on how to obtain access to these datasets. | NA-MIC Driving Biological Projects investigators have made several datasets available to NA-MIC developers. This page provides information on how to obtain access to these datasets. | ||
| − | = | + | == Accessing NA-MIC Data == |
| + | |||
| + | ''BIRN Controlled Infrastructure'' | ||
| + | |||
| + | FMRI and DTI datasets are currently available to NAMIC participants via the BIRN Controlled Infrastructure. In order to access this data, please use the following steps to create a BIRN account with NAMIC permissions: | ||
| + | |||
| + | * ** Go to the [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=apply portal] and follow directions to set up a member account (Your site may not be listed - please state that you are a NA-MIC participant in the interest section) | ||
| + | |||
| + | * ** Then [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=myActivitiesPortlet&gs_action=handleMembershipRequests&Fnf_action=Request+Membership&up=Fnf&Fnf_projectID=3 request NAMIC related permissions]. See the [[DataRepository#Notes|Notes section]] for more information. | ||
| + | |||
| + | |||
| + | * ** Before you download data using the account you have created, please confirm with your PI that you have received adequate human subject training. If your site does not provide this training, please do this [https://www.citiprogram.org/registerselectinstitution.asp?strKeyID=9934456536544677479770 Human Subject Online Training] as an affiliate of Brigham and Women's Hospital and send a copy of your certificate to your PI for their records. | ||
| + | |||
| + | ''Search for NAMIC Data'' | ||
| + | |||
| + | Users earch for data available on the BIRN data grid through metadata applied to the data itself. Each data object and collection can be assigned any number of metadata tags. Currently the metadata tags consist of items such as: Modality (DTI, T1, T2, etc.), Institution, etc. | ||
| + | |||
| + | To see an example of metadata on a data file, take a look at the following UCI file: First | ||
| + | * Ensure you aare logged into the [https://portal.nbirn.net Portal] | ||
| + | * Then view the [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&up=21I&21I_dirpath=%2Fhome%2FProjects%2FStudy5000__0005%2FFiles%2FArchive&JavaScript=enabled contents of that archive] | ||
| + | * Then to search for data, click the Query Metadata button [[image:Tango_search_metadata_large.png]] | ||
| + | |||
| + | ''Replication of Data'' | ||
| + | |||
| + | Currently, the NAMIC data sets are stored in BIRN at: | ||
| + | |||
| + | /home/Projects/NAMIC__0003/Files (physicall located at NCMIR) <br /> /home/Projects/Study5000__0005/Files (physically located at UCI) | ||
| + | |||
| + | For redundancy in case a Birn Rack were to go offline we have replicated the data to the BWH rack in preparation for the Programmer's Week. | ||
| + | |||
| + | This can be seen when using 'Sls -a' | ||
| + | |||
| + | [jgerk@ncmir-gpop scratch]$ Sls -a UCI07110773.tgz | ||
| + | jgerk 0 z-ucsd-ncmir-nas1 451315092 2005-02-18-14.00 % /home/Projects/Study5000__0005/Files/Archive/UCI07110773.tgz | ||
| + | jgerk 1 z-harvard-bwh-nas1 451315092 2005-06-24-17.02 % /home/Projects/Study5000__0005/Files/Archive/UCI07110773.tgz | ||
| + | |||
| + | During regular use it is not important that the file resides in two places, but it should be understood that removing the file will result in removing both copies. | ||
| + | |||
| + | As more data is added to NAMIC we can periodically run the following command to update the BWH resource (provided you have the correct permissions). | ||
| + | |||
| + | Sbkupsrb -r -S z-harvard-bwh-nas1 Files | ||
| + | |||
{| cellpadding="10" | {| cellpadding="10" | ||
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== [[DataRepositoryHarvard|Brockton VA/Harvard Structural and DTI Images]] == | == [[DataRepositoryHarvard|Brockton VA/Harvard Structural and DTI Images]] == | ||
| + | |||
| + | |||
| + | |- | ||
| + | |||
| + | | | [[Image:NAMIC UncinateFasiculus prelim.jpg|200px]] | ||
| + | | | | ||
| + | |||
| + | == [[DataRepositoryDartmouth|Dartmouth Data and Images]] == | ||
| + | |||
| + | |- | ||
| + | |||
| + | | | [[Image:MBIRNseedROIcc1.png|200px]] | ||
| + | | | | ||
| + | |||
| + | == [[DataRepositoryIrvine|Irvine Data and Images]] == | ||
| + | |||
| + | |} | ||
Latest revision as of 16:25, 11 April 2023
Home < DataRepositoryNewBack to Resources Page
Overview of Data Repository
NA-MIC Driving Biological Projects investigators have made several datasets available to NA-MIC developers. This page provides information on how to obtain access to these datasets.
Accessing NA-MIC Data
BIRN Controlled Infrastructure
FMRI and DTI datasets are currently available to NAMIC participants via the BIRN Controlled Infrastructure. In order to access this data, please use the following steps to create a BIRN account with NAMIC permissions:
- ** Go to the portal and follow directions to set up a member account (Your site may not be listed - please state that you are a NA-MIC participant in the interest section)
- ** Then request NAMIC related permissions. See the Notes section for more information.
- ** Before you download data using the account you have created, please confirm with your PI that you have received adequate human subject training. If your site does not provide this training, please do this Human Subject Online Training as an affiliate of Brigham and Women's Hospital and send a copy of your certificate to your PI for their records.
Search for NAMIC Data
Users earch for data available on the BIRN data grid through metadata applied to the data itself. Each data object and collection can be assigned any number of metadata tags. Currently the metadata tags consist of items such as: Modality (DTI, T1, T2, etc.), Institution, etc.
To see an example of metadata on a data file, take a look at the following UCI file: First
- Ensure you aare logged into the Portal
- Then view the contents of that archive
- Then to search for data, click the Query Metadata button
Replication of Data
Currently, the NAMIC data sets are stored in BIRN at:
/home/Projects/NAMIC__0003/Files (physicall located at NCMIR)
/home/Projects/Study5000__0005/Files (physically located at UCI)
For redundancy in case a Birn Rack were to go offline we have replicated the data to the BWH rack in preparation for the Programmer's Week.
This can be seen when using 'Sls -a'
[jgerk@ncmir-gpop scratch]$ Sls -a UCI07110773.tgz jgerk 0 z-ucsd-ncmir-nas1 451315092 2005-02-18-14.00 % /home/Projects/Study5000__0005/Files/Archive/UCI07110773.tgz jgerk 1 z-harvard-bwh-nas1 451315092 2005-06-24-17.02 % /home/Projects/Study5000__0005/Files/Archive/UCI07110773.tgz
During regular use it is not important that the file resides in two places, but it should be understood that removing the file will result in removing both copies.
As more data is added to NAMIC we can periodically run the following command to update the BWH resource (provided you have the correct permissions).
Sbkupsrb -r -S z-harvard-bwh-nas1 Files
|
Brockton VA/Harvard Structural and DTI Images |
|
Dartmouth Data and Images |
|
Irvine Data and Images |
