hi michael,
there is a toolbox for spm by jesper andersson which will correct for the
subject moving during the aquisition of all the diffusion-weighted images
and the b0 images. so suppose you did 10 diffusion-weigthed and 4 b0 images.
after this movement correction you will get the a file which is the mean of
the b0 images nicely put in the same space as the 10 diffusion weighted
images. try to normalize that mean b0 image to the EPI template (or create
your own T2 tamplate) and then apply the *sn_3d.mat files to your
corresponding FA maps.
in your step three you mention a segmentation. do you mean segmenting the FA
maps? if so then i don't think that is needed. for one, jepser's toolbox
will smooth the FA maps for you (and you can set how much smoothing you wish
for) and secondly when you do your analysis later in spm you can set an
absolute threshold. usually, setting this threshold to 0.15 confines the the
analysis well to voxels which contain white matter (i.e. 0 =< FA =< 1 so not
considering voxels with FA < 0.15 cuts out those voxels in the ventricles
and most of gray matter).
this is the way i would do it. hopefully others will also answer your
question and then you can make a more educated decision as to how to go
about your analysis. good luck.
zoltan
**********************************
Zoltan Nagy
Karolinska Institutet
Neonatology
Astrid Lindgrens Barnsjukhus Q2:07
171 76 Stockholm, Sweden
Phone: +46-8-517-77354
Fax: +46-8-517-77353
E-mail: [log in to unmask]
**********************************
----- Original Message -----
From: "Michael Yassa, B.A." <[log in to unmask]>
To: <[log in to unmask]>
Sent: Tuesday, December 30, 2003 12:18 AM
Subject: VBM on DTI data
Dear SPMers,
I am trying to conduct a comparison between patients and controls using VBM
on DTI data. I have a single FA image for each subject that only includes
brain matter, and everything outside the brain is masked out.. What would be
the best way to process this data for VBM? Since this data is already
skull-stripped, I assume that I will not need to segment and brain extract
before normalization.
The sequence of steps I had in mind is as follows:
1. Coregister FA maps in AIR
2. Normalize to EPI template in SPM
3. Create tissue segments... I'm not sure if this segmentation routine is
dependent on intensity or priors. If someone could elaborate on this
further, that would be great. Also, it would make sense not to correct for
intensity inhomogeneities at this step, but I cannot be sure.
4. Smooth white matter segments
5. Use smoothed WM segments for statistical comparison.
I'm not sure if this is the correct way to perform this analysis, and I'm
not sure how John's scripts would react to FA maps as opposed to T1
anatomicals.
Any feedback regarding this would be sincerely appreciated.
Mike
--
Michael A. Yassa, B.A. Psychiatric Neuro-Imaging
Sr Research Technician JHU School of Medicine
Tel: 410-955-7861 600 N. Wolfe St.
Fax: 410-614-3676 Phipps 322
Email: [log in to unmask] Baltimore MD 21287
|