These instructions are preliminary; we are awaiting Iain's confirmation of some details. But I believe this to be correct.
(1) First we must Import the data into a MEDx folder in the proper directory structure. 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 the last 160 .IMA files into the folder; i.e., skip the first three .IMA files. (In Open Image, set File Format to AutoDetect.)
(8) Name the group of 160 images Comp.
(9) Save the folder with a name following the convention SubjectID.v1.Comp.f, and exit MEDx.
(10) Invoke the hs2 program.
(11) Under Select Processing Protocol, select the protocol named /export/w/apps/tcl/Comp_ProtocolFile.txt. This should be entry #38 in the list.
(12) 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 Process Folders button, and hs2 will process the 160 images. Results will be placed in a new Results directory as usual.
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