[MINC-users] 6-parameter fitting with minctracc

[Claude LEPAGE]

Hi Jim,

> BTW, as these are ADNI
> scans, they've also already had one run through of N3 (off topic, but
> related).

Last summer, we had a meeting to sort out the differences with
your CIVET output of ADNI and Alex' output. Those differences
were very substantial. It turned out that Alex used the raw 
native images while you used the pre-processed ADNI images. 
The pre-processing steps included gradient corrections, B1
field correction (to account for multi-site acquisitions), 
and finally some N3. Since ADNI has some scans at 3T (N3 with
spline distance of 50mm) and some scans at 1.5T (N3 with
spline distance of 200mm), the ADNI people decided to take a
weighted average of the 1.5T and 3T scans and run N3 at an
intermediate spline distance of 150mm, which is wrong for 
both 1.5T and 3T. It was clear in my recommendations that you
should not use the N3-corrected images provided by ADNI, but
use only the images after the corrections for the site. I don't
know if this will solve the problem with the cortical thickness
values in the motor area, but you should try this. Alan and Alex
also received a copy of my recommendations for this study.

Claude