Motion Correction

(1) In the MEDx folder, click on the Toolbox button (it has an icon that looks like a hammer and pliers). This will pop up the Toolbox window.

(2) In the Toolbox window, select Registration --> AIR.... This will pop up the Automated Image Registration (v3.08) dialog box.

(3) In the Automated Image Registration (v3.08) dialog box, click on the Select... button that is on the same level as Standard Image. This will pop up a dialog box entitled Select Page; select the Instance Number: 6 image volume in the List of Pages (this image is now the first of 84 scans in the data set), and then click on the OK button.

(4) In the Automated Image Registration (v3.08) dialog box, click on the Select... button that is on the same level as Reslice Group or Image. This will pop up a dialog box entitled Select Page. Click on the checkbutton next to Groups, and then select the group corresponding to the set of 84 scans (this should be the only group in the List of Pages). Then click on the OK button.

(5) In the Automated Image Registration (v3.08) dialog box, under Registration Type, select Intramodality.

(6) Let's find a threshold based on the maximum value in the first image. In the group page for the 84 scans, click on the button corresponding to the Instance Number: 6 image volume in the List of Pages (again, this image is now the first of 84 scans in the data set); this will display the first image. Select Display --> Display Range..., and in the Display Range dialog box click on the Compute button. The number under Max should be 1118. If we use a 15% threshold, then 15% of this is about 168.

These thresholds will be applied to their respective image volumes to remove background noise outside the brain, effectively masking the two image volumes. This prevents noise from being used as data in the registration process.

(7) Back in the Automated Image Registration (v3.08) dialog box, under Thresholds, set both Standard Image and Reslice Image to 168. (We are assuming that the rest of the 83 scans have about the same intensity range.)

(8) Under Algorithm and Model, leave Algorithm set to Linear, and leave Model set to Rigid Body (6 parameter model). Click on the OK button. AIR will start aligning all of the scans to the first scan (the Instance Number: 6 image volume). When AIR is done running, you should have a new group of 84 scans, which are the motion-corrected scans. Note that the name of the group contains the phrase Motion Correction of.... Let's save these out to disk, because if the MEDx folder gets too full MEDx begins to run very slowly. (I think this is because the memory managemenent in MEDx is inefficient.)

(9) In the main MEDx window, select File --> ImageScript Execution.... This pops up the ImageScript Execution dialog box. Make sure that you're looking at the Group page with the icons for the 84 motion-corrected scans (whose name contains the phrase Motion Correction of...). This is because the SaveNSetAVW.tcl script works only on the current page, i.e., the page that you are currently looking at. (A few MEDx functions operate in this manner, which is something to keep in mind. When performing a MEDx operation, ask yourself how MEDx knows which image or group to perform the operation on.)

(10) In the ImageScript Execution dialog box, either type

into the Script File entry box, or browse to it by clicking on the little button with the folder icon. Then click on the OK button. This will pop up the Save AVW Files dialog box.

(11) In the Save AVW Files dialog box, set Directory to wherever you created your tutorial directory, e.g.

Set Root Name to whatever you like, e.g.

(The "Mc" indicates Motion Corrected. To avoid later confusion, try to embed pertinent information such as image type, contrast, and thresholds into your file names.) Set X Scale and Y Scale to 3, and Z Scale to 2.996 (these are voxel sizes in mm). Be sure that you are looking at the Group page for the 84 scans, rather than at the page of a single scan. (This script runs only on the current page!) Then click on the OK button. The 84 motion-corrected images will be written into the tutorial directory in AVW format. (I have heard that this is a slight error in nomenclature in MEDx. Apparently, it really should be called Analyze format; AVW is a software toolbox that is closely associated with the Analyze software, but is not itself a format. Or so I have heard.)

The script will display the 84 scans as it's writing them out to disk, one after the other. Pay attention -- make sure that the images look okay! I.e., make sure that they aren't blank or distorted.

(12) When the script is done, select File --> Exit MEDx in the main MEDx window. You'll probably get a dialog box asking whether you want to save the folder. Click on the Discard Changes button. This exits MEDx.

The next step is to perform Make a Mean Image Volume and Mask.

For more information on using AIR in MEDx, see section 19.5 in Chapter 19 of the MEDx's User's Guide, and section 31.6 in Chapter 31. See also this stand-alone tutorial on using AIR in MEDx. Here is the official AIR website.

For comparison, check out this tutorial on motion correction in SPM96.

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