Melonakos at 21:37, 12 December 2009

2009-12-12T21:37:09Z

Melonakos at 20:08, 23 June 2008

2008-06-23T20:08:52Z

Melonakos: New page: Back to NA-MIC Data NOTOC = DBP 1 Data = Several sources have made data available for medical image computing research. This page contains a list of data available from DBP...

2008-06-23T18:41:41Z

New page: Back to NA-MIC Data __NOTOC__ = DBP 1 Data = Several sources have made data available for medical image computing research. This page contains a list of data available from DBP...

New page

Back to [[Data|NA-MIC Data]]
__NOTOC__
= DBP 1 Data =

Several sources have made data available for medical image computing research. This page contains a list of data available from DBP 1 sites. For general information regarding accessing NA-MIC data, click [[Data:DownloadInstructions|here]].

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== '''Dartmouth Structural, Functional, T2 and DTI Images''' ==

=== Data Access ===

To download this data, click on the following links:
* Ensure that you are logged into the [https://portal.nbirn.net portal]
* [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&aBS_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FDartmouth%2FHealthyControls6&up=aBS&JavaScript=enabled 6 Healthy Controls]
* [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&M13_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FDartmouth%2FSchizophrenia15&up=M13&JavaScript=enabled 15 SZ]

=== Data Description ===

* 6 Healthy Controls Data
** All data were acquired on a 1.5T GE MRI Scanner using the Horizon LX software platform.
** SPGR: [[Dartmouth_SPGR_Scan_Parameters|Scan Parameters and Data Structure]]
** T2: [[Dartmouth_T2_Scan_Parameters|Scan Parameters and Data Structure]]
** fMRI (ER-RECOG task):[[Dartmouth_fMRI_Scan_Parameters|Scan Parameters and Data Structure]]
*** NOTE: onsets for tasks included with data are WRONG. New onsets have been uploaded to [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&Hwv_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FDartmouth%2FHealthyControls6&up=Hwv&JavaScript=enabled here]
** DTI:[[Dartmouth_DTI_Scan_Parameters|Scan Parameters and Data Structure]]
*** The slices of the 3rd and the 6th datasets are in IS order, i.e., the first slice is the inferior most slice. The slices of the rest 4 datasets are in SI order.
*** Dartmouth DTI Protocol for Slicer can be found here: [[NAMIC-Dartmouth-2b12g-Volume_Protocol_File|Dartmouth Slicer Protocol]]
*** Converting the dicom images into nrrd format using [[NAMIC-Dartmouth-DWI-to-NRRD-Format|a simple MATLAB script]], and [[NAMIC-Dartmouth-nrrdheader|a sample nrrd header]]
*** Without any MATLAB or other pre-processing: [[NAMIC-Dartmouth-DWI|NRRD headers which use existing slice images from tar files]] and which can be loaded directly into Slicer
** Hippocampus Traces: Hippocampal traces were made on an SPGR resampled to 1.015625 mm3 isotropic voxels and realigned along the long axis of the hippocampus. This reoriented SPGR volume is included with the traces. Traces were drawn using the ''Brains'' program.
** Hippocampal ROIs: Binary Hippocampal ROIs have been uploaded in the same directory as the traces. These ROIs are in Analyze format. There are four ROIs for each subject (left hippo, left hippo smoothed 3mm FHMW, right hippo, right hippo smoothed 3mm FHMW). The smoothed ROIs have 'sROI' in the filename.
* MRI Data for 15 SZ
** Data consists of DICOM slices for SPGR and trace files for various Frontal Lobe Subdivisions
*** SPGR: [[Dartmouth_SPGR_Scan_Parameters_Schiz|Scan Parameters and Data Structure]]
*** Frontal Traces: Traces were made on SPGR volume using the ''Brains'' program. Go [[Frontal_Structure_Listing|here]] for a listing of the structures available and the filenames associated with them.

=== Data Contact ===

* For any extra information needed on this data please contact John D. West. Contact info can be found on the members list in the NA-MIC section of BIRN.

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== '''Brockton VA/Harvard Structural and DTI Images''' ==

=== Data Access ===

To download this data, click on the following links:

* Ensure you are logged into the portal [https://portal.nbirn.net portal]
* Download [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&CPq_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FHarvard%2Farchive_morph&up=CPq&JavaScript=enabled Structural MRI]
* Download [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&up=7li&7li_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FHarvard%2Farchive_diffusion&JavaScript=enabled DTI data]
** '''The header for each DWI file is obsolete and incorrect, download Harvard_VA_nhdr.tgz and overwrite the DWI nrrd headers'''

=== Data Description ===

* '''Structural Data Description'''
** [[Brockton_MRI_Scan_Parameters|Scan Parameters and Description of Files]]
** [[DBP:Harvard:MorphROI|Regions of Interest Description and References]]
* '''DTI Data Description'''
** [[Brockton_DTI_Scan_Parameters|Scan Parameters and description of files]]
** [[DBP:Harvard:DTIROI|Regions of Interest Description and References]]
* [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&zBx_dirpath=%2Fhome%2FProjects%2FNAMIC__0003%2FFiles%2FHarvard%2Fdocs&up=zBx&JavaScript=enabled Spreadsheets giving diagnosis, gender, age of subjects as well as information about the different structure delineated]

=== Data Contact ===

If you have any questions about the data, please contact Sylvain Bouix at Harvard.

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== '''UCI Structural, Functional and PET Images, Genetic and Clinical Data''' ==

=== Data Access ===

To download this data:
* First make sure you are logged into the portal
* Then go to the [https://portal.nbirn.net:443/gridsphere/gridsphere?cid=srbfilebrowser&gs_action=gotoDirectory&up=21I&21I_dirpath=%2Fhome%2FProjects%2FStudy5000__0005%2FFiles%2FArchive&JavaScript=enabled Study5000 data directory]

=== Data Description ===

* [[UCI_fMRI_Dir_Struct|Directory Structure and Naming Conventions ]]
* Papers to be uploaded.
* MRI
** [[UCI_MRI_Scan_Parameters|Scan Parameters]]
* fMRI
** [[UCI_fMRI_Scan_Parameters|Scan Parameters]]
** [[UCIfMRIscans|Sample memory task data on Schizophrenics: (N=28 Sz)]]
* PET
** [[UCI_PET_Scan_Parameters|Scan Parameters]]

=== Data Contact ===

* For additional information on this data, please contact Jessica Turner at UCI.

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== '''Toronto Genetics Data''' ==

Coming Soon!!!

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Data:DBP1 - Revision history

Melonakos at 21:37, 12 December 2009

Melonakos at 20:08, 23 June 2008

Melonakos: New page: Back to NA-MIC Data __NOTOC__ = DBP 1 Data = Several sources have made data available for medical image computing research. This page contains a list of data available from DBP...

Melonakos: New page: Back to NA-MIC Data NOTOC = DBP 1 Data = Several sources have made data available for medical image computing research. This page contains a list of data available from DBP...