|
|
| (8 intermediate revisions by 3 users not shown) |
| Line 1: |
Line 1: |
| − | =Introduction=
| + | <big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/SlicerOnBIRN here]</font></big> |
| − | NA-MIC uses the BIRN infrastructure to store some data sets provided by Core 3. Some of those data sets are only for internal use by NA-MIC participants. There are also data sets that are available for anybody to use in their research. This page explains how to
| |
| − | | |
| − | * get an account for BIRN
| |
| − | ** if you are a NA-MIC participant
| |
| − | ** if you are not a NA-MIC participant
| |
| − | * find NA-MIC data on portal
| |
| − | * find available non-NA-MIC data on the portal
| |
| − | * launch Slicer from the portal to view the data
| |
| − | | |
| − | =Getting a BIRN Portal Account=
| |
| − | | |
| − | [[image:portal-main.png|150px|thumb|Portal Main page]]
| |
| − | | |
| − | Visit the BIRN Portal, and click the tab labelled "Request an account". Fill out the appropriate information. Your account application will be reviewed by a human and verified. When your account has been accepted, you will be emailed an "activation link". Click on this link to view the portal as a registered user. The entire process usually takes less than a day. When logged in, you should be taken to the "My Space" page, which represents all of the projects that you have access to.
| |
| − | | |
| − | [[image:portal-logged-in.png|150px|thumb|Logged in to the BIRN Portal]]
| |
| − | | |
| − | =Getting access to NAMIC data=
| |
| − | | |
| − | NAMIC data is stored as part of the "NAMIC" project within the BIRN Portal. In order to get access to the data, you need to be a member of the NAMIC project. If NAMIC is listed in your projects from your "My Space" page, you need to take no further action. If it is not listed, you simply need to join.
| |
| − | | |
| − | Visit the overall BIRN Projects page by clicking the "Projects" link in the "Collaboration" tab's submenu.
| |
| − | | |
| − | [[image:projects-tab.png|150px|thumb|BIRN Portal projects page]]
| |
| − | | |
| − | Search for the NAMIC project---the easiest approach is to hit ^F or Cmd-F (Mac) and type NAMIC.
| |
| − | | |
| − | [[image:namic-project.png|150px|thumb|NAMIC Project entry]]
| |
| − | | |
| − | On the right hand side is a column "Membership?". Click the "Request" link. You will receive an email stating that you have requested membership into the project.
| |
| − | | |
| − | [[image:membership-request.png|150px|thumb|Requesting admission to the NAMIC project]]
| |
| − | | |
| − | When the project administrator has viewed your request and approved you, you will receive an email that you have been accepted into the project. Visiting the portal will allow you to complete the cycle, by clicking the "Accept" link.
| |
| − | | |
| − | [[image:membership-request-accepted.png|150px|thumb|Accepted into the NAMIC project]]
| |
| − | | |
| − | =Searching NAMIC data=
| |
| − | | |
| − | From the "My Space" section, click on the NAMIC project in your "Projects Overview" tab.
| |
| − | [[image:namic-project-space.png|150px|thumb|NAMIC Project space]]
| |
| − | | |
| − | Select "SRB Project Folders". From here, either browse for specific data (if you know what you're looking for) or search by meta data.
| |
| − | | |
| − | [[image:namic-file-space.png|150px|thumb|SRB File Space for NAMIC project]]
| |
| − | | |
| − | Use the MetaDataUtils to search for files of a particular type. Select the "search" icon [[image:Search-icon.png]]. Search on any of the following fields.
| |
| − | | |
| − | DataStatus \in (1---meaning?)
| |
| − | | |
| − | Institution (obvious)
| |
| − | | |
| − | ScannerField <=> field strength, in Tesla
| |
| − | | |
| − | ScannerManufacturer (obvious)
| |
| − | | |
| − | ScannerModel (one of Echospeed...)
| |
| − | | |
| − | ScannerScanType (DTI (others?))
| |
| − | | |
| − | SubjectDiagnosis (one of Unknown...)
| |
| − | | |
| − | SubjectGroup (One of Unknown...)
| |
| − | | |
| − | =Searching for non-NAMIC Data=
| |
| − | | |
| − | From the Data Management tab, simply visit the project home directory of whatever project you are interested in. If the data is public, you will be able to view it. If the data is not public (and you don't see it), please request access to that project using similar steps to above. You can search for data using the metadata search utilities described above.
| |
