View source for 2011 Summer Project Week Iowa Huntington's disease data sharing

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<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:NAMIC_HD_Xnat_Interface.png|Screenshot of xnat interface for NAMIC_HD project
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'''Full Title of Project'''

==Key Investigators==
* UIowa: Hans Johson, Mark Scully


==Data Files==
*[[File:Anonymized_factorsExternalIDs_with_blage_mriDate_scanID_daysSince.xlsx]]
*[[File:NAMIC%2BFactors.doc]]
*[[File:NAMIC_HD_DWI_DTI.xlsx]]
*[[File:NAMIC_HD_DataDescription.pdf]]
*[[File:ANN_Segmentation_thesis.pdf]]
*[[File:20111102_ANNSegmentation.pptx]]

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<h3>Objective</h3>
Share a subset of the Huntington's disease data from UIowa.

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<h3>Approach, Plan</h3>
Data will be made available via xnat.

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<h3>Progress</h3>
Data is shared as the NAMIC_HD project on xnat at https://predict-hd.net/xnat.

Fill out the form [[File:NAMIC_DATA_SHARING.doc]] to request access.

In addition to the raw data anonymized factors relating to the disease and three different reconstructions have been made available.  The anonymized factors are available in the File:NAMIC_HD_DataDescription.pdf file in the data files section above.  The first reconstruction is the output of the BRAINS AutoWorkup pipeline run in June.  The second is the pipeline run 2011-09 with improved segementations.  The third is the DWI data after processing.  The reconstructions are explained in the above data files.

After access has been granted and an account has been created you can fetch the raw data using the script [[File:Fetch_NAMIC_HD_data.sh.gz]] and the processed data using [[File:Fetch_NAMIC_HD_derived_data.sh.gz]].

The raw data is large (over 1TB) so it will take a long time and require a large amount of space.

Run either script with '-h' for terse help.  Each file takes a basePath under which the output will be constructed of the form $basePath/NAMIC_HD/subjectID/scanID.zip for the raw data and $basePath/NAMIC_HD/subjectID/scanID_type.zip for the processed data.  The raw data zip files expand to scanID/scans/scanTypes/resources/DICOM/files/ and the processed zip files expand to scanID/reconstructions/scanID_10_AUTO.NN3Tv20110419-BRAINSAutoWorkup/out/resources/resourceType/files/.  When fetching the raw data you can specify a list of image types you are interested in using '-t' followed by a comma delimited list of scan types (It defaults to 'ALL'). You can get a list of possible scan types by running "./Fetch_NAMIC_HD_DATA.sh -l".  The types you are likely to be interested in are at the beginning of the list.  If either script is interrupted while running it can be restarted and it will skip over already downloaded zip files (provided you have not set force=True or deleted the relevant .zip files).  If you run either command without a required input you will be prompted to provide it.  Brief usage examples for each command follows:

usage: ./fetch_NAMIC_HD_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-l (list) List scan types and exit.<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>
-t scanTypes: comma delimited list of scan types. (Defaults to ALL) Ex: T1-30,T2-30<br>


usage: ./fetch_NAMIC_HD_derived_data.sh [-u username] [-b basePath] [-t scanTypes] [-f]<br>
-f (force) Overwrite .zip files even if they exist. (defaults to FALSE)<br>
-u username: username on predict-hd.net/xnat<br>
-b basePath: path to store data under<br>


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==References==

==Delivery Mechanism==

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This work will be delivered to the NAMIC Kit as a project in the xnat instance at https://predict-hd.net/xnat