Hi Jason,
Your ROI should be in the standard space. You can register the MRIco
template to the standard and apply the transformation to the ROI you
drew using flirt. It should only take a minute to do this. Then they
can be used for pre-threshold masking.
As for statistical power, if you run the analysis uncorrected, you will
not gain anything from using the ROI. the ROI will improve you
statistic al power during the correction for multiple comparisons.
Generally speaking, cluster thresholding is less stringent than the
voxel wise correction. If you anticipate highly significant very small
activations, for example, nuclei in the brain stem, a voxel wise
correction works best.
As for what type of ROI you would like to use, I can only offer an
opinion. I generally prefer to use irregularly shaped ROI which follow
the underlying anatomy. I am also generally more inclusive than
exclusive. The statistical gain made by reducing the number of voxels
is small compared to failing to search a brain area that is in fact
significantly active. If you are very concerned about reducing the
number of voxels, I would recommend a hypothesis driven limit
(excluding ROI that you have weak hypotheses about).
Also, I always view my uncorrected data. I find it is useful to see
everything that may be going on with my experiment.
i hope this is helpful!
Best
jen
Jennifer Bramen
UCLA Brain Mapping Center
660 Charles Young Dr. So
Los Angeles, CA 90095
On May 18, 2004, at 8:27 AM, Jason Steffener wrote:
> Hello,
> I have two groups of subjects
> and would like to investigate task related signal chaneg in each group
> seperately and to ultimately use an unpaired t-test to compare the two
> groups.
>
> I would like to limit my search to only a few regions of interest. I
> have
> drawn the rois on the MRIcro standard image which has voxel sizes of
> 1x1x1
> with a matrix of 181x217x181. Can I use these ROIs as pre-threshold
> masking in the higher level FEAT analysis?
> or
> Does my ROI image need to have the same dimensions and voxel sizes as
> the
> FSL standard? (2x2x2, 91 109 91)
>
> What should my threshold be then when I use the pre-threshold masking?
> voxel wise, cluster wise, uncorrected? I would guess voxel wise.
>
> Also in regards to the resels issue. My ROIs have a large surface area
> and
> should therefore limit the statistical power gained by limiting my
> search
> volume. Is there some tradeoff I should make? Could I make nonspecific
> "smooth blob" rois that encompass my regions of interest. An ideal ROI
> in
> this case would then be a sphere, but what about cubes or 3-D ellipses?
>
> Any pointers are greatly appreciated.
> best regards,
> Jason.
>
> Jason Steffener
> Department of Radiology
> New Jersey Medical School
> Biomedical Engineering Department
> New Jersey Institute of Technology
> Newark, NJ USA
> (973) 676-1000 x1545
> http://web.njit.edu/~jrs3
>
>
Jennifer Bramen
UCLA Brain Mapping Center
660 Charles Young Dr. So
Los Angeles, CA 90095
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