mrAlign4 User's Guide
Objective:
Running mrAlign rotates the inplane anatomy slices from your functional scan in order to align them to your reference volume anatomy. This is done in order to preserve the location of regions of activity across scans done in separate scanning sessions. The following are instructions on how to do an automatic alignment.
Notes to the user:
1) This current version of mrAlign4 is not fully tested.
2) This version of mrAlign4 may not work well for all data sets. It tends to work well on axial inplanes and some coronal inplanes. Unfortunately, oblique inplanes usually do not align well . So why is this useful to you? In mrAlign3, you had to tediously rotate and translate the interpolated inplanes in order to get your coarse alignment. But mrAlign4 does this automatically. Therefore, you can use mrAlign4 to get your initial coarse alignment, save this data, and then use mrAlign3 to get a final alignment. Ideally, this should save you some time.
3) If you already have a bestrotvol from mrAlign3 that you are happy with, I would NOT suggest running mrAlign4 on that data set since the result you get will not be any better than before.
4) Also, unless you select the “Save Alignment (bestrotvol)” option from the File menu, mrAlign4 will NOT modify any of your previously existing data. Therefore, even if you run mrAlign4 and get a bad result, you will not have altered your data unless you select “Save Alignment (bestrotvol).”
5) Please email Sunjay ( slad@stanford.edu ) if you try this out and let him know how well it works/doesn't work for you …
Getting Started
- Run Matlab and cd to the directory named with the date of the scan you want to align.
- At prompt, type mrAlign4
Suggested steps for axial and some coronal inplanes:
Step 1 - Coarse Alignment
- In the File menu, select the “ Extract Coarse Alignment From Header Files ” option.
- Assuming your subject's vAnatomy Ifiles are in the proper location (maroon/a1/anatomy/ subject's_name /Ifiles), all the Ifiles will be found automatically. However, if the subject's Ifiles are located somewhere else, you will be prompted to specify the location of the first Ifile (I.001) for the vAnatomy.
- mrAlign4 then automatically determines a coarse rotation and translation.
Step 2 - Checking the Coarse Alignment (optional)
- In the Check Alignment menu, select the “ Check Alignment (all slices) ” option.
- Select “ Yes ” to correct image intensity.
- This displays three images: original inplane on top, interpolated inplane (with the coarse alignment applied) on bottom, a checkerboard of the two in the middle. Chances are these images will not be well aligned. But this is just an initial check to see if the Coarse Alignment got you close.
- Hit space bar to view the next slice.
Step 3 – Final Automatic Alignment
- In the Compute Alignment menu, select the “ Compute Automatic Alignment (coarse and fine iterations) ” option.
- mrAlign4 will perform 10 'iterations' in an attempt to make an alignment. If after 10 iterations, an alignment has not been able to be computed, you will be prompted to choose whether or not you wish the program to perform another 10 iterations.
- Allow it to run to at least 30 iterations. From my tests, mrAlign4 tends to take between 6 and 24 iterations, depending on the image quality and accuracy of the coarse alignment.
- If the alignment has not been computed after 30 iterations, you should not proceed. This is probably a data set that needs to be aligned with mrAlign3 (see “Suggested steps for oblique inplanes” below).
Step 4 – Checking the Final Alignment
- In the Check Alignment menu, select the “ Check Alignment (all slices) ” option.
- Select “ Yes ” to correct image intensity.
- This displays three images: original inplane on top, interpolated inplane on bottom, a checkerboard of the two in the middle. Examine the checks for continuity. Try to follow sulci from one check to the next. Check that the edge of the skull lines up neatly. Note that some features (e.g., veins) might look very different (bright in one image and dark in the other). The amazing thing is that mrAlign deals with this pretty well (at this point, you owe Oscar a few kegs of beer).
- Hit space bar to view the next slice.
Step 5 – Saving the Alignment
· In the File menu, select the “ Save Alignment (bestrotvol) ” option.
· This saves a “bestrotvol.mat” in the current directory.
Suggested steps for oblique inplanes:
Step 1 - Coarse Alignment
- In the File menu, select the “ Extract Coarse Alignment From Header Files ” option.
- Assuming your subject's vAnatomy Ifiles are in the proper location (maroon/a1/anatomy/ subject's_name /Ifiles), all the Ifiles will be found automatically. However, if the subject's Ifiles are located somewhere else, you will be prompted to specify the location of the first Ifile (I.001) for the vAnatomy.
- mrAlign4 then automatically determines a coarse rotation and translation.
Step 2 - Checking the Coarse Alignment (optional)
- In the Check Alignment menu, select the “ Check Alignment (all slices) ” option.
- Select “ Yes ” to correct image intensity.
- This displays three images: original inplane on top, interpolated inplane (with the coarse alignment applied) on bottom, a checkerboard of the two in the middle. Chances are these images will not be well aligned. But this is just an initial check to see if the Coarse Alignment got you close.
- Hit space bar to view the next slice.
- If this initial check looks close, mrAlign4 might work so try using Steps 3 - 5 as noted above .
- If this initial check does not look close, mrAlign4 will probably fail so proceed with Steps 3 - 4 as noted below .
Step 3 – Save the Coarse Alignment
· In the File menu, select the “ Save Alignment (bestrotvol) ” option.
- This saves the coarse alignment as “bestrotvol.mat” in the current directory.
- In the File menu, select the “ Quit ” option.
Step 4 – Use mrAlign3
- At the Matlab prompt, type mrAlign3 .
- In the File menu, select the “ Load Alignment (bestrotvol) ” option.
- Then proceed as you normally would in mrAlign3. You will still have to rotate and translate the inplanes before running the final automatic alignment, but hopefully it will be a little easier since mrAlign4 got you somewhere close.
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