Hi Jennifer,
You don't need to use FEAT for doing vertex analysis with FIRST.
You just need to create a design matrix with the GLM GUI.
For your case it is simply a single column/regressor/EV which
is -1 for controls and +1 for patients. Note that using 0's and 1's
would also work, as FIRST demeans any input. Once you've
set this up in the GLM GUI then save it and use the design.mat
file that it creates as an input. There's a practical in the FSL course
that covers this (in the segmentation section) which you might
want to look at (with or without downloading the data).
As for bias correction, you can do this with FAST. There is an
option (-B) which saves the bias corrected output image.
Note that you need to run BET on your image before this. We
also have a VBM implementation that you could use, but
the output should also be suitable for SPM.
All the best,
Mark
On 27 Nov 2008, at 23:46, Jennifer Addicks wrote:
> Hello,
>
> I have 2 questions:
>
> 1. Can anyone explain how to set up the design.mat file to enter into
> the scripts for shape and volumetric analyses for FSL First. I want to
> compare hippocampal volumes in patient and control groups with an
> independent samples t-test. I am unclear how to use FEAT with
> structural data and I am having trouble figuring this out with the FSL
> website.
>
> 2. I was wondering if anyone could quickly explain or provide me with
> the script to
> do bias correction on structural T1 images with N3 (non-parametric
> non-uniformity intensity normalization) in FreeSurfer. I have brain
> extracted images (BET-fsl) which I need to bias correct and then feed
> into SPM5 for VBM (using the pipeline recommended by Acosta-Cabronero
> et al 08).
>
> Any help would be appreciated.
> Thanks,
>
> Jennifer Phillips BSc, MSc (Cand.)
> Graduate Student
> Department of Neuroscience, University of Ottawa
> Mood Disorders Research Unit, University of Ottawa Institute of Mental
> Health Research
> 1145 Carling Ave, Research Tower, Room 6412
> Ottawa, Ontario K1Z 7K4
> Tel: 613.722.6521 x.6188
> Fax: 613.798.2982
> [log in to unmask]
> www.imhr.ca
>
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