[caret-users] Freesurfer to Caret scripts: Trouble with talairach.xfm (MNI transform too big)

Donna Dierker donna at brainvis.wustl.edu
Tue Nov 10 09:28:16 CST 2009

Because there are several users following the progress of these scripts, 
I wanted to alert them to an issue I came across yesterday.

I was underwhelmed with the quality of one of the hemispheres 
auto-landmarks, and I suspected it might be due to the 711-2B fit being 

While it's too soon to hang the auto-landmark problem on that cause, I 
did confirm that the orig.711-2B.nii volume being produced is bigger 
than the typical 711-2B bounding box.  Backing upstream, I confirmed the 
MNI transform exceeds the typical MNI bounding box.  The 
B12flirt_on_flirt.jpg illustrates how the mean PALS_B12 surface looks 
overlaid on the MeanBuckner12_FLIRT volume.  The fit looks good.  The 
B12flirt_on_orig.mni.jpg shows the same mean PALS_B12 surface overlaid 
on my subject's orig volume, as transformed to MNI using the 
talairach.xfm.  The volume bleeds out much further in all directions, 
but is especially noticeable near the occipital pole.

It could be a bad talairach.xfm, or it could be my processing sequence 
(e.g., the reslicing to LPI somehow?).

I don't want to brush this off, so I'll need a bit of time to study it.

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