[MINC-users] 6-parameter fitting with minctracc

EJ Nikelski nikelski at bic.mni.mcgill.ca
Sun Feb 21 13:57:50 EST 2010


Hi Claude,

   Yup, I recall the meeting last summer, and I'll be certain to use
the non-N3-corrected scans for all future analyses.  Having said that,
the low tissue contrast issues have also been reported by Jason Lerch
in his MACACC paper, and can also be seen in the ICBM-152 dataset
verification images, so - as you suggested - what I am seeing is
likely not primarily an ADNI N3 issue.

   I'm very curious to determine precisely how many acquisitions one
needs before the thickness values in the motor cortex stabilize.  I
would also like to state explicitly that I do *not* believe that this
tissue contrast issue is Civet/Insect-specific.  Other studies
interested in dorsal cortex, using other tools (e.g., FreeSurfer),
routinely use > 1 scans ... sometimes quite a few more.

Thanks,

-Jim


On Sun, Feb 21, 2010 at 8:12 AM, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
> 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University


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