Home < Slicer4:Download Data

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: