Slicer4:Download Data

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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

	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.
	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.
	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

• 

  lupus001_T1.nii.gz
  128x256x256 voxels
  registered and bias corrected T1 series
  5.7MB - uploaded on 2010-08-10 19:35:20 by XXX
  Download, download with mrml

• 

  lupus002_FLAIR_reg+bias.nii.gz
  128x256x256 voxels
  registered and bias corrected Flair acquisition
  4.86MB - uploaded on 2010-08-10 19:35:20 by xxxx
  Download, download with mrml

• 

  lupus003_T2_reg+bias.nii.gz
  192x256x256 voxels
  registered and bias corrected T2 wieghted image
  6.34MB - uploaded on 2010-08-10 19:35:20 by xxxx
  Download, download with mrml

• 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

• 

  lupus001_T1.nii.gz
  128x256x256 voxels
  registered and bias corrected T1 series
  5.7MB - uploaded on 2010-08-10 19:35:20 by XXX
  Download, download with mrml

• 

  lupus002_FLAIR_reg+bias.nii.gz
  128x256x256 voxels
  registered and bias corrected Flair acquisition
  4.86MB - uploaded on 2010-08-10 19:35:20 by xxxx
  Download, download with mrml

• 

  lupus003_T2_reg+bias.nii.gz
  192x256x256 voxels
  registered and bias corrected T2 wieghted image
  6.34MB - uploaded on 2010-08-10 19:35:20 by xxxx
  Download, download with mrml

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

• Collection level

• Manage thumbnails

How to link a template to a resource

First, go resource edit page:

Then select the template you want to use:

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:

Click on "Upload Files":

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

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

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:

How to change a thumbnail

First, go the an item page:

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

Select the thumbnail you want to change:

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

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