Difference between revisions of "Connecting to SRB BIRN"
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The connection parameters that must be used to connect to SRB BIRN from inside MIPAV are slightly different from the parameters which you used to connect to the NDAR portal. To obtain these parameters, | The connection parameters that must be used to connect to SRB BIRN from inside MIPAV are slightly different from the parameters which you used to connect to the NDAR portal. To obtain these parameters, | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 From the NDAR portal page, navigate to the Data Management tab;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Click the GridInfo icon. See | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 From the NDAR portal page, navigate to the Data Management tab;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Click the GridInfo icon. See Figure 5<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 The info page appears displaying different sets of parameters;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 You need those which appear under General SRB User Parameter;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 5 Open MIPAV, and then call File>SRB BIRN>Open Image from SRB;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 6 The Connect to dialog box appears;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 7 Enter parameters from General SRB User Parameter into the dialog box. Refer to Figure 3<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 8 In the Authentication list box, select ENCRIPT1;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 9 Press Connect, to connect to SRB server. The SRB File Chooser dialog should appear displaying the list of catalogs. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 10 Open the desired catalog and select a file of interest. Press Open to open the file. See Figure 4.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 11 The file now should be opened in MIPAV. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> |
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 3. Parameters used to connect to SRB BIRN from inside MIPAV. <br /></font>'''</div> |
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[[Image:SRB_GeneralUserParameters.jpg]] | [[Image:SRB_GeneralUserParameters.jpg]] | ||
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− | As shown in | + | As shown in Figure 3 the following parameters are used to connect to SRB: |
<div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | ||
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<div class="CellBody">Home Directory</div> | <div class="CellBody">Home Directory</div> | ||
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 4. The SRB FIle Chooser dialog box.<br /></font>'''</div> |
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[[Image:SRB_fileChooser.jpg]] | [[Image:SRB_fileChooser.jpg]] | ||
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==== Uploading files to SRB BIRN ==== | ==== Uploading files to SRB BIRN ==== |
Revision as of 18:50, 10 February 2012
Connecting to SRB BIRN
In this chapter . . .
- "Requesting the SRB account"
- "Setting MIPAV SRB options and opening files"
- "Setting the SRB connection parameters"
- "Uploading files to SRB BIRN"
- "Transferring files from MIPAV to SRB BIRN and vise versa"
- "Set up the NDAR pipeline"
- "Saving files to SRB"
Biomedical Informatics Research Network(BIRN, http://www.nbirn.net/) is a shared biomedical IT infrastructure supported by NIH, which hastens the process of new understanding and treatment of disease through use of distributed knowledge. BIRN supports collaboration between groups with different expertise and resources (e.g., technical, scientific, social and political). The Storage Resource Broker (SRB), developed at SDSC, is a client-server middleware designed for managing file collections in a heterogeneous, distributed environment. All files within the environment are part of a single data grid BIRN file system where a file's logical location within the file system is represented independently of its physical location. The SRB middleware is capable of managing large data sets and is currently managing the BIRN data grid.
Get Connected to SRB BIRN
To be able to connect to SRB BIRN from inside MIPAV and open the image files using SRB you need to:
Requesting the SRB account
Setting MIPAV SRB options and opening files
To set up the MIPAV SRB options:
Setting the SRB connection parameters
The connection parameters that must be used to connect to SRB BIRN from inside MIPAV are slightly different from the parameters which you used to connect to the NDAR portal. To obtain these parameters,
As shown in Figure 3 the following parameters are used to connect to SRB:
General SRB User Parameter
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MIPAV
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Host
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Host
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Port
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Port
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User Name
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Name
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Home Directory
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user Domain
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Domain
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Default Resource
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Storage Resource
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Uploading files to SRB BIRN
To test your access to SRB BIRN from inside MIPAV, you might choose to upload a couple of files to your home catalog, first. In order to do that,
Later, you can upload your image files to SRB BIRN from MIPAV using the SRB Transfer and Save to SRB menus.
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Transferring files from MIPAV to SRB BIRN and vise versa
To transfer files from MIPAV to SRB BIRN and back to MIPAV:
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Set up the NDAR pipeline
You can run MIPAV scripts on the DICOM images stored on the DICOM server and automatically save results to the chosen SRB BIRN catalogue.
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In order to be able to do that, you should establish the NDAR pipeline, first.
The script you choose should be run on the DICOM files and the results stored in the chosen SRB directory.
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Saving files to SRB
To save your image file directly to SRB:
The file should now appear in the chosen catalog.
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