Hi Jesper,
I have uploaded the GM_mod_merge file to #803202. The first 30 volumes are
from controls, and the following 40 are from various subject groups. The
controls and subjects are age and sex matched.
Thanks for looking at it.
I did the cropping to remove neck and to get quicker (and hopefully better)
results from bet.
I'm surprised that you are not surprised at the result of my experiment.
Why would the fslvbm output from one subject appear different after changing
only the input image dimensions? It is the same brain.
I look forward to your thoughts.
J
----- Original Message -----
From: "Jesper Andersson" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Thursday, June 17, 2010 3:08 PM
Subject: Re: [FSL] FSL-VBM vs Freesurfer
> Dear Jay,
>
>> I've discovered something of interest...
>>
>> I mentioned that I used fslroi to crop the images prior to bias
>> correcting
>> and bet-ing. I had asked if the differing image sizes would be an issue
>> for
>> fslvbm, and Gwenaelle replied that it would not.
>>
>> Since you seemed surprised that my subject volumes looked quite
>> different
>> from each other in the GM_mod_merg file, I have run an experiment using
>> one
>> subject only, a copy of that subject, and a version of that subject
>> cropped differently.
>> The original and copy look identical after processing through the fslvbm
>> scripts, however the newly cropped volume is visibly different from the
>> other 2!
>>
>> Clearly the cropping introduces some alteration, and the widely
>> different cropping
>> parameters for my subjects my seems have contributed to the visible
>> differences. I
>> used the non-linear version of registration btw...would affine been a
>> better choice?
>
> I am not surprised you find a difference, but I would have thought that
> the results you get with cropping would be the better ones. The main way
> in which cropping will affect your results (apart from reducing
> processing time and disk space) is by allowing BET to do a better job.
>
> Maybe by now it is better if you uploaded the mod_merge file so we can
> have a look at it.
>
> Jesper
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