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Analysis of Beijing Data for R01 - September 2006

Page history last edited by PBworks 14 years, 2 months ago

These instructions are preliminary; we are awaiting Iain's confirmation of some details. But I believe this to be correct.


 

First we must Import the data into a MEDx folder in the proper directory structure.

 

(1) Create a Study directory for this quick project (analysis for the R01). I'd recommend creating it somewhere in /export/w/Research_Studies/Beijing or /export/w/Research_Studies/Beijing/BeijingData.

 

(2) Within the Study directory, consider creating two directories, one for grade1 and one for grade4, with the intention of creating the Subject directories in these grade directories. If you think this is too much fuss, you can just create the Subject directories directly in the Study directory, as long as their directory names don't conflict.

 

(3) Create a Subject directory (e.g., K37_s70 or s70) within the proper grade directory or directly within the Study directory, whichever way you have chosen to go.

 

(4) Create a directory named Visit1 in the Subject directory.

 

(5) Create a directory named Folders in the Visit1 directory.

 

(6) Invoke MEDx and open up a new folder.

 

(7) Load all of the .IMA files into the folder except for the first three. (In Open Image, set File Format to AutoDetect.) After the images are loaded, you should see only 160 of them in the MEDx folder (not 163!!).

 

(8) Name the group of 160 images Comp (not comp!!).

 

(9) Save the folder in the Folders directory created in step 5 with a name following the convention "SubjectID.v1.Comp.f". SubjectID can be anything that represents this particular subject (e.g., K37_s70 or s70), but don't capitalize the v in v1; and do capitalize the c in Comp.

 

(10) Exit MEDx.


 

Now perform the first-level within-subject analysis.

 

(11) Invoke the hs2 program.

 

(12) Under Select Processing Protocol, select the protocol named /export/w/apps/tcl/Comp_ProtocolFile.txt. This should be entry #39 in the list.

 

(13) Under First Level Analysis, click on the Add Folder/Directory button and browse to the MEDx folder you saved in step 8. After selecting the folder, click on the OK button.

 

(14) Click on the Process Folders button, and hs2 will process the 160 images. Results will be placed in a new Results subdirectory.

 

(15) Proceed as usual with the RunAirOnSubjects.csh and RemoveScansWith_0.6mm_MovementAndReanalyze.csh scripts.


 

When the first-level analysis has been done on all of the HK subjects, then proceed to perform within-group analyses on the HK data.

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