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Set up

Page history last edited by PBworks 16 years, 10 months ago

Set up

For this tutorial, we'll be using data from subject #39540. It is possible that you have already obtained data for this subject via DICOM transfer before; if so, it may lead to confusion in the DICOM transfer step of this tutorial.


To prevent confusion, let's first clear out any files from previous DICOM transfers of this subject.


(1) First, determine your Query/Retrieve directory. Run the following command:


grep UserDicomQRDir ~/.MEDxdefaults


You should get something that looks like this:


/UserDicomQRDir (/export/home/myHomeDir/DICOM)


indicating that your Query/Retrieve directory is, e.g., /export/home/myHomeDir/DICOM.


If you get an error message that the .MEDxdefaults file doesn't exist, or if you get only the Unix prompt back, you need to set up your .MEDxdefaults file. The easiest way to do this is to copy it from somebody else's home directory (for whom DICOM is working) into your own home directory. But if you do this, you'll probably want to point your Query/Retrieve directory to your own directory.


On the other hand, it occurs to me just now that it might be okay for everybody to use a common directory for the Query/Retrieve directory. Further, it might be okay for everybody to set it to /tmp, which is cleared every time the machine is rebooted! Periodically clearing the Query/Retrieve directory might actually be desirable -- see step 3 below.


(2) Go into the Query/Retrieve directory, and list the contents. E.g.,


cd /export/home/myHomeDir/DICOM



(3) If you see a subdirectory named CSL395_20050809, it is a directory containing files from previous DICOM transfers of this subject. To prevent confusion, delete this directory, e.g.:


rm -rf CSL395_20050809


Incidentally, if you use MEDx's DICOM transfer to obtain multiple fMRI runs from the same subject, you might notice that when you try to obtain the 2nd run you'll get not only the 2nd run but also the 1st run. And when you try to obtain the 3rd run, you'll also get the first two runs; etc. I think this is a bug in MEDx. If you find this annoying, a trick you can do is to remove the subject's directory in between retrievals, like we did in step 3 above. You might even want to periodically clear your entire Query/Retrieve directory, e.g.


rm -rf /export/home/myHomeDir/DICOM/*


Don't forget the '*' at the end! It might be nice for the Query/Retrieve directory to be empty, but it needs to exist for DICOM Q/R to work!


The next step in this tutorial is: Obtain data for tutorial via DICOM transfer.


See Section 8.3 of Chapter 8 of the MEDx User's Guide for further information on DICOM defaults in MEDx.


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