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The current discussion on VBM was just in time when I am setting up a
workflow to process data on patients with a disease which has been proposed with
cerebral atrophy. I list my workflow here hoping that I am doing things right
and anyone could give me some instructions.
My study involved with a total of 76 T1 MPRAGE images (voxel size
1*1*1) with 46 patients and 30 healthy controls (all female).
1.
Raw images were firstly imported by Mricron to produce skull stripped
images.
2.
Segmented with the New Segment routine in SPM8.
3.
The rest is exactly the same as described "Using DARTEL" in the SPM8
manual, using rc1.nii and rc2.nii files to create template, then using Normalize
to MNI Space to move the original c1.nii and c2.nii files into MNI
space.
4.
For covariates, as gender is not a issue in my
case and patients were proposed to have brain atrophy, I think using the
total volume of GM as the covariate would be appropriate; the age of
subjects were across 16 to 45 (matched), then I will use age as a covariate
as well.
5.
For statistics, I'll use a explicit brain mask to exclude any
weird behavior in the margin areas, a 2 sample t-test was firstly used to see if
any significant difference between groups, then I would like to
correlate the individual volume in the significantly differed areas,
if any, with duration of disease and some serum antibodies.
I also have some doubts as
follows:
1.
Recent VBM with DARTEL studies [1-3] in neuroimage were still
using SPM5 rather than SPM8, is using SPM
2.
The preprocessing of DARTEL were proposed to achieve optimal results
with skull stripped and bias corrected in FSL [1, 4], however, as a rookie in
neuroimaging softwares, I don¡¯t know how to manipulate FSL on the process. Then
I alternatively used Mricron to get the skull stripped images. Will such a
process jeopardize the study?
3.
To get the total volume of GM, instruction from ¡°Obtaining Globals¡±
in http://en.wikibooks.org/wiki/SPM/VBM#Interpreting_Results
suggests using
¡°get_totals¡±. I have no clue how to do this in the interface of matlab or SPM8,
can anyone kindly give me some detailed steps?
Any suggestion is greatly
appreciated!
Thank you in advance.
Lin Yun
1.
Pereira, J.M., et al., Registration accuracy for VBM studies varies
according to region and degenerative disease grouping. NeuroImage, 2010. 49(3): p.
2205-15.
2.
Kosaka, H., et al., Smaller insula
and inferior frontal volumes in young adults with pervasive developmental
disorders. NeuroImage, 2010. 50(4): p.
1357-63.
3.
Bergouignan, L., et al., Can voxel
based morphometry, manual segmentation and automated segmentation equally detect
hippocampal volume differences in acute depression? NeuroImage, 2009. 45(1): p.
29-37.
4.
Acosta-Cabronero, J., et al., The
impact of skull-stripping and radio-frequency bias correction on grey-matter
segmentation for voxel-based morphometry. NeuroImage, 2008. 39(4): p.
1654-65.