Difference between revisions of "Slicer4:Download Data"

From Slicer Wiki
Jump to: navigation, search
 
(12 intermediate revisions by the same user not shown)
Line 52: Line 52:
 
*A. Support for local customization  
 
*A. Support for local customization  
  
1.  Add SQL schemas to link a resource to a template.  '''Done'''
+
'''1.''' Add SQL schemas to link a resource to a template.  '''Done'''
  
2.  Add support for administrators to create/edit links between resources  
+
'''2.''' Add support for administrators to create/edit links between resources  
 
templates. '''Done'''
 
templates. '''Done'''
  
3.  Modify the core MIDAS to support templates at the resource level. '''Done''' (communities, collections)
+
'''3.''' Modify the core MIDAS to support templates at the resource level. '''Done''' (communities, collections)
  
 
*B. Specific Customization for NAMIC datasets  
 
*B. Specific Customization for NAMIC datasets  
1.  Display of the download page at the “collection” level according to the layout
+
'''1.''' Display of the download page at the “collection” level according to the layout
 
the wiki.  
 
the wiki.  
 +
 
-Layout : '''Done'''
 
-Layout : '''Done'''
 +
 
-Download All: '''Done'''
 
-Download All: '''Done'''
 +
 
-Download All with mrml: '''Done'''
 
-Download All with mrml: '''Done'''
 +
 
-Download single bitstream: '''Done'''
 
-Download single bitstream: '''Done'''
 +
 
-Download single bitstream with mrml: '''Done'''
 
-Download single bitstream with mrml: '''Done'''
-Download single resource: '''In progress (70%)'''
+
 
-Download single resource with mrml: '''To do'''
+
-Download single resource: '''Done'''
 +
 
 +
-Download single resource with mrml: '''Done'''
 +
 
 
-Show Items information: '''Done'''
 
-Show Items information: '''Done'''
 +
 
-Show Bitstreams Metadata: '''Done'''
 
-Show Bitstreams Metadata: '''Done'''
2.  Support for manually replacing a thumbnails '''In progress (80%)'''
 
  
3Implementation of javascript support to extend description on mouse over. '''Done''' (community page)
+
'''2.''' Support for manually replacing a thumbnails '''Done'''
  
*C. Testing phase'''To do'''
+
'''3.'''  Implementation of javascript support to extend description on mouse over. '''Done''' (community page)
  
*D. Upgrade of the MIDAS server '''To do'''
+
*C. Testing phase '''Done'''
  
'''Screenshot'''
+
*D. Upgrade of the MIDAS server '''Done'''
 +
 
 +
== Demo ==
 +
 
 +
http://insight-journal.org/midas/collection/view/171
 +
 
 +
== Screenshots ==
  
 
*Community level  
 
*Community level  
Line 87: Line 101:
 
*Manage thumbnails
 
*Manage thumbnails
 
[[File:Midas-slicer-screenshot3.jpg|200px]]
 
[[File:Midas-slicer-screenshot3.jpg|200px]]
 +
 +
== How to link a template to a resource==
 +
First, go resource edit page:
 +
 +
[[File:Midas-slicer-screenshot-link0.jpg|400px]]
 +
 +
Then select the template you want to use:
 +
 +
[[File:Midas-slicer-screenshot-link1.jpg|400px]]
 +
 +
You can recursively apply the template. (All the children of the resource will use the selected template)
 +
 +
== How to upload new files==
 +
First, go a collection page and create an item:
 +
 +
[[File:Midas-slicer-screenshot-upload0.jpg|400px]]
 +
 +
Click on "Upload Files":
 +
 +
[[File:Midas-slicer-screenshot-upload1.jpg|400px]]
 +
 +
Select the files you want to upload (you can select multiple files)
 +
 +
[[File:Midas-slicer-screenshot-upload2.jpg|400px]]
 +
 +
If Midas warns you that a file is too big, use the "large files" tool:
 +
 +
[[File:Midas-slicer-screenshot-upload4.jpg|400px]]
 +
 +
When your files are uploaded, you can ask midas to create resources. If you do that, Midas will analyze the selected files and try to find the metadata:
 +
 +
[[File:Midas-slicer-screenshot-upload5.jpg|400px]]
 +
 +
== How to change a thumbnail==
 +
First, go the an item page:
 +
 +
[[File:Midas-slicer-screenshot2bis.jpg|400px]]
 +
 +
Then go a the menu and click on "thumbnails":
 +
 +
[[File:Midas-slicer-screenshot4.jpg|400px]]
 +
 +
Select the thumbnail you want to change:
 +
 +
[[File:Midas-slicer-screenshot3.jpg|400px]]
 +
 +
Upload a new image (the application will resize the image)
 +
 +
[[File:Midas-slicer-screenshot5.jpg|400px]]
 +
 +
If you like the new thumbnail, click on "Set thumbnail" to finalize the modification
 +
 +
[[File:Midas-slicer-screenshot6.jpg|400px]]

Latest revision as of 09:05, 29 June 2011

Home < Slicer4:Download Data

Back to Slicer 4 Developer Projects

Introduction

  • This is a first generation mock-up for a database display/download schema for Slicer
  • The NA-MIC download data can be used for prototyping.
  • thumbnails should be extracted for now from the center slice of the volume. Mechanism to replace manually. Down the road, we will use the thumbnail from the mrml file.
  • Annotation should be extracted from the DICOM headers, if available. We will need a painless way to edit the annotation (with wiki style history). Once the slicer annotation module is working (summer 2011), we can extract information from there.
  • Pack as many thumbnails as possible horizontally (based on width of browser window and font size)
  • Only list one or two lines of text, the rest pops up on rollover.
  • Pack densly, use space sparingly

Top Level

Schiz-thumb.png Brain: Multi-modality (sMRI, DTI, fMRI) from Schizophrenia Study

There are 20 cases: ten are Normal Controls and ten are Schizophrenic. Each case includes a weighted T1 scan, a weighted T2 scan, an fMRI scan, a DTI volume, the DWI with 51 directions, and several masks and labelmaps. Available from Harvard.

Child-i.png Brain: 2-4 Year Old from Autism Study

Data for 2 autistic children and 2 normal controls (male, female) scanned at 2 years with follow up at 4 years from a 1.5T Siemens scanner. Files include structural data, tissue segmentation label map and subcortical structures segmentation. Available from UNC.

Lupus-i.png Brain: White Matter Lesions for Lupus Study

Data for 5 cases of Lupus White Matter Lesion patients. The data is co-registered. Each case contains: T1-weighted, T2-weighted, FLAIR, and masks for brain and lesions. Available from MIND.

One Level Down

  • Case 1, study 1
    • Lupus001
    • last update on 2010-04-12 14:32:11 (13.4 MB in 8 files)
    • Brain MRI study of a subject with slight Lupus Erythematodes.
    • Download this study: Just the data, data with a mrml file for Slicer 3.6
  • Case 1, study 2
    • Lupus002
    • last update on 2010-04-12 14:32:11 (13.4 MB in 8 files)
    • Brain MRI study of a subject with severe Lupus Erythematodes.
    • Download this study: Just the data, data with a mrml file for Slicer 3.6


Development status

  • A. Support for local customization

1. Add SQL schemas to link a resource to a template. Done

2. Add support for administrators to create/edit links between resources templates. Done

3. Modify the core MIDAS to support templates at the resource level. Done (communities, collections)

  • B. Specific Customization for NAMIC datasets

1. Display of the download page at the “collection” level according to the layout the wiki.

-Layout : Done

-Download All: Done

-Download All with mrml: Done

-Download single bitstream: Done

-Download single bitstream with mrml: Done

-Download single resource: Done

-Download single resource with mrml: Done

-Show Items information: Done

-Show Bitstreams Metadata: Done

2. Support for manually replacing a thumbnails Done

3. Implementation of javascript support to extend description on mouse over. Done (community page)

  • C. Testing phase Done
  • D. Upgrade of the MIDAS server Done

Demo

http://insight-journal.org/midas/collection/view/171

Screenshots

  • Community level

Midas-slicer-screenshot1.jpg

  • Collection level

Midas-slicer-screenshot2.jpg

  • Manage thumbnails

Midas-slicer-screenshot3.jpg

How to link a template to a resource

First, go resource edit page:

Midas-slicer-screenshot-link0.jpg

Then select the template you want to use:

Midas-slicer-screenshot-link1.jpg

You can recursively apply the template. (All the children of the resource will use the selected template)

How to upload new files

First, go a collection page and create an item:

Midas-slicer-screenshot-upload0.jpg

Click on "Upload Files":

Midas-slicer-screenshot-upload1.jpg

Select the files you want to upload (you can select multiple files)

Midas-slicer-screenshot-upload2.jpg

If Midas warns you that a file is too big, use the "large files" tool:

Midas-slicer-screenshot-upload4.jpg

When your files are uploaded, you can ask midas to create resources. If you do that, Midas will analyze the selected files and try to find the metadata:

Midas-slicer-screenshot-upload5.jpg

How to change a thumbnail

First, go the an item page:

Midas-slicer-screenshot2bis.jpg

Then go a the menu and click on "thumbnails":

Midas-slicer-screenshot4.jpg

Select the thumbnail you want to change:

Midas-slicer-screenshot3.jpg

Upload a new image (the application will resize the image)

Midas-slicer-screenshot5.jpg

If you like the new thumbnail, click on "Set thumbnail" to finalize the modification

Midas-slicer-screenshot6.jpg