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Automatically Fixing the Talairach Transform

When you have a bad Talairach transform, you should first attempt to fix it automatically before resorting to a manual registration.

Gray Scale Variations

If you suspect that the bad transform might have been caused by a gray scale problem, first try running mri_convert with "T1" (white matter set to have 110 only) and then "brain" like this (run these commands in the <subject name>/mri directory):

mri_convert T1.mgz T1.mnc
mritotal -protocol icbm T1.mnc T1.xfm

Check the transform using tkmedit or by looking at the 'Final objective function value' output as the last line of the mritotal command (a number bigger than 0.1 is suspect). If the transform is still bad, try:

mri_convert brain.mgz brain.mnc
mritotal -protocol icbm brain.mnc brain.xfm

Again, check the transform using tkmedit or noting the final objective function value. A reminder: to check a transform, load the volume into tkmedit, and in the tkmedit toolbar, go to:

File -> Transforms -> Load Transform for Main Volume...

Click browse, select the file transforms/talairach.xfm and click 'OK' to select the original transform, or select one of the new transforms, such as T1.xfm or brain.xfm (being sure to select File -> Transforms -> Unload Transform for Main Volume if one was loaded prior).

If you find a good transform using the step above, replace mri/transforms/talairach.xfm with the good one (either using 'T1.xfm' or 'brain.xfm', whichever produced better results). You must use the name talairach.xfm.

If you would like to experiment with these commands, sample data that is known to be quite badly aligned is found in the sample data set directory: buckner_data/tutorial_subjs/095_talairach_before/mri/orig.

Bright Neck Region

If you suspect that the bad transform is the result of a bright neck region, edit the volume to erase the neck and run mritotal on the edited volume. This can be accomplished through simple volume editing: set all the regions to zero where y is greater than a certain value (around 170). This generally works better than using the brain volume. Check your transform using tkmedit.


2010-02-06 17:59