Difference between revisions of "Slicer3:Remote Data Handling"

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'''[[Slicer3:Developers#Slicer_3_Projects | Back to Slicer3 Projects List ]]'''
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<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Remote_Data_Handling  here]</font></big>
 
 
 
 
 
 
= ITK-based mechanism handling remote data (for command line modules, batch processing, and grid processing) =
 
 
 
= vtkMRMLStorageNode methods for handling remote data (for loading and saving data for interactive use) =
 
 
 
The first goal is to figure out what workflows to support, and a good implementation approach.
 
 
 
Currently, '''Load Scene''', '''Import Scene''', and '''Add Data''' options in Slicer all encapsulate two steps:
 
* locating a dataset, usually accomplished through a file browser, and
 
* selecting a dataset to initiate loading.
 
 
 
For loading remote datasets, the following options are available:
 
* break these two steps apart explicitly,
 
* bind them together under the hood,
 
* or support both of these paradigms.
 
 
 
==Breaking apart "find data" and "load data":==
 
 
 
'''Possible workflow A'''
 
* User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
 
* From the Load Scene file browser, user selects the .xcat or .xml archive. If no locally cached versions exist, each remote file listed in the archive is downloaded to /tmp directory (always locally cached) by the Download Manager, and then loaded into Slicer via a vtkMRMLStorageNode method when download is complete.
 
 
 
'''Possible workflow B'''
 
* User downloads .xcat or .xml (MRML) file to disk using the HID or an XNAT web interface
 
* From the Load Scene file browser, user selects the .xcat or .xml archive. If no locally cached versions exist, each remote file in the archive is downloaded to /tmp (only if a flag is set) by the Download Manager, and loaded directly into Slicer via a vtkMRMLStorageNode method when download is complete.
 
 
 
'''Possible workflow C'''
 
* User locates a MRML file, .xcat archive, or individual dataset on the HID or an XNAT web interface
 
* User types the uri into the ''Load Scene'', ''Import Scene'', or ''Add Data'' interfaces.
 
* If no locally cached versions exist, each remote file in the archive is cached to /tmp by the Download Manager, and loaded directly into Slicer via a vtkMRMLStorageNode method when download is complete.
 
 
 
==Bundling together "find data" and "load data":==
 
 
 
'''Possible workflow D'''
 
 
 
In this workflow, Slicer would make calls to HID or XNAT webservices to determine what data of interest is available... Questions:
 
* How might this work?
 
* Do we really want to re-implement functionality in the HID web interface?
 
* Maybe Slicer can implement a workflow (A-C) but also offer a simplified BIRN query interface that has functionality like:
 
** Request BIRNIDs for all subjects who have a complete FIPS/FreeSurfer analysis
 
** Request an xcat for one of these BIRNIDs
 
 
 
== Saving Data back to remote site ==
 
* Since we have no plan for where to save MRML files on HID, can we have a webservices function we can call from Slicer that writes a file to /dev/null on HID in the meanwhile?
 
 
 
== What data do we need in an .xcat file? ==
 
For the fBIRN QueryAtlas use case, we need a combination of '''FreeSurfer morphology analysis''' and a '''FIPS analysis''' of the same subject. With the combined data in Slicer, we can view activation overlays co-registered to and overlayed onto the high resolution structural MRI using the FIPS analysis, and determine the names of brain regions where activations occur using the co-registered morphology analysis.
 
 
 
The xcede2.0 catalog should contain to associated collections of data for the fBIRN QueryAtlas use case:
 
 
 
    * One FreeSurfer "lh" model and one FreeSurfer "rh" model at most
 
    * the FreeSurfer structural brain.mgz image volume
 
    * the FreeSurfer example functional example_func.nii
 
    * some FIPS-generated Statistical volumes
 
    * the FreeSurfer aparc+aseg.mgz label map volume
 
    * the FreeSurfer lh.aparc.annot annotation file
 
    * the matrix to align the example_func + statistics to the brain.mgz: anat2exf.register.dat
 
 
 
These are found in the following places, according to the default FIPS/FreeSurfer directory structure.
 
 
 
The BIRN HID webservices shouldn't really need to know the subset of data that QueryAtlas needs... maybe the web interface can take a BIRN ID and create a FIPS/FreeSurfer xcede catalog with all FIPS/FreeSurfer uris, and Slicer can parse out the ones of interest, and download them?
 
 
 
[[ Slicer3:XCEDE_use_cases | See this page for more discussion of Slicer's use of Xcede catalogs ]]
 
 
 
= Asynchronous I/O Manager =
 

Latest revision as of 18:07, 10 July 2017

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Note: We are migrating this content to the slicer.org domain - The newer page is here