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Obtain data for tutorial via DICOM transfer

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

Obtain data for tutorial via DICOM transfer

(1) Make a directory for your tutorial. Perhaps make it in your home directory, e.g.


mkdir /export/home/myHomeDir/tutorial


In this tutorial, I'll use subject #39540's Implicit Reading 1 data. If you like, you can try some other subject's Implicit Reading 1 data.


(2) Bring up MEDx, open up a New Folder, then select Image --> DICOM --> Query/Retrieve...


(3) For "Patient Last Name", type in




(4) Click on the Query button. Two entries for 2005-08-09 will appear in the white panel, corresponding to two DICOM Studies.


(5) Double-click on the first entry (Study ID 1) to see the Series within this Study. This will pop up the Series tab, and a list of Series.


(6) Find the entry with Description ep2d Implicit Reading 1, using the scrollbar if necessary. Single-click on this entry; it will become highlighted in blue. Then click on the Retrieve button. A dialog box will appear, asking you whether you really want to proceed; click on the Yes button. MEDx's Busy button will turn red, indicating that MEDx is busy. After about a minute, the MEDx folder should display a new Group page containing 89 buttons, corresponding to 89 image volumes.


Make sure that the images look okay! Do not assume that everything is hunky-dory. Make sure that the images aren't blank or distorted. Click on one of these buttons to look at the image volume. If it looks blank, it could simply be a display issue that is easily fixed by adjusting the windowing level. Select Display --> Display Range..., and then in the Display Range window click on the Compute button. Under Min and Max, the minimum and maximum values of the image will be displayed. These are good numbers to know about the image. Select Image --> Image Properties.... Note that the XYZ dimensions of the image are 64 x 64 x 64 (Width, Height, and Slices), that there are 16 bits per pixel, and that the Pixel Encoding is Signed (I think it really should say Signed Integer). These are also good pieces of information to know about an image.


When processing fMRI data, you need to always pay attention, and question what you are seeing. You must always ask yourself whether what you're seeing makes sense. As Robert Savoy has said, "Functional MRI is difficult."


Click on the U-turn button (has an icon of a U-turn arrow) to return to the group page, and click on another image volume button. When you have looked at a few scans and are satisfied that they look okay, return to the Group page containing 89 buttons.


(7) The first five scans are "dummy scans" which we'll exclude from the analysis. Select Page --> Page Manager.... This will pop up the Page Manager dialog box. Grab and drag the corners and/or edges of this window to widen it.


(8) In the Page Manager dialog box, you'll see a list of all of the pages in the current MEDx folder. In particular, you'll see a bunch of them with the phrase "Instance Number: 1", "Instance Number: 2", etc. They should go all the way to 89, corresponding to 89 fMRI scans acquired. Click on "Instance Number: 1"; it should become highlighted in blue. Then, while pressing the Shift key on the keyboard, click on "Instance Number: 5"; the first five Instance Numbers should now be highlighted.


(9) Click on the Delete button. A confirmation box will pop up; click on the OK button to confirm.


This will delete the first five scans from the MEDx folder.


You are now ready to proceed to Motion Correction.


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


Here is a stand-alone MEDx tutorial on DICOM. If DICOM in MEDx is already working for you, skip steps 1-10 in this tutorial. You don't want to be messing with your DICOM defaults if they are working. If it ain't broke, don't fix it.


Return to tutorial main page

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