|
|
| (339 intermediate revisions by 4 users not shown) |
| Line 1: |
Line 1: |
| − | '''[[Slicer3:Developers#Slicer_3_Projects | Back to Slicer3 Projects List ]]''' | + | <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) --Nicole =
| |
| − | | |
| − | = vtkMRMLStorageNode methods for handling remote data (for loading and saving data for interactive use) --Wendy =
| |
| − | | |
| − | 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 required analyses including all derived data are probably in two different locations on the HID (check with Burak). The analysis output is stored to local disk using a standard directory structure. | |
| − | | |
| − | ===FIPS analysis (.feat) directory and required data===
| |
| − | For instance, one FIPS output directory is called sirp-hp65-stc-to7-gam.feat. Under this directory, QueryAtlas needs the following datasets:
| |
| − | * sirp-hp65-stc-to7-gam.feat/reg/example_func.nii
| |
| − | * sirp-hp65-stc-to7-gam.feat/reg/freesurfer/anat2exf.register.dat
| |
| − | * sirp-hp65-stc-to7-gam.feat/stats/(all statistics files of interest)
| |
| − | * sirp-hp65-stc-to7-gam.feat/design.gif (this image relates statistics files to experimental conditions)
| |
| − | | |
| − | ===FreeSurfer analysis directory, and required data ===
| |
| − | For instance, one FreeSurfer morphology analysis directory is called fbph2-000670986943. Under this directory, QueryAtlas needs the following datasets:
| |
| − | | |
| − | * fbph2-000670986943/mri/brain.mgz
| |
| − | * fbph2-000670986943/mri/aparc+aseg.mgz
| |
| − | * fbph2-000670986943/surf/lh.pial
| |
| − | * fbph2-000670986943/surf/rh.pial
| |
| − | * fbph2-000670986943/label/lh.aparc.annot
| |
| − | * fbph2-000670986943/label/rh.aparc.annot
| |
| − | | |
| − | == What do we want HID webservices to provide? ==
| |
| − | | |
| − | | |
| − | | |
| − | * 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 uris in the FIPS and FreeSurfer directories, and QueryAtlas can find the relevant ones and download that subset of data.
| |
| − | | |
| − | * Then, for each uri in a catalog (or .xml MRML file), we need to be able to download programmatically using http:// or ftp:// etc. '''We are assuming all datasets are publicly readable.'''
| |
| − | | |
| − | [[ Slicer3:XCEDE_use_cases | See this page for more discussion of QueryAtlas's current use of Xcede catalogs, and assumptions... ]]
| |
| − | | |
| − | = Asynchronous I/O Manager --Wendy =
| |
