Hi Martin,
You may want instead to run the GLM on the whole volume & simply apply the
ROI as a mask at the results stage, (or try using marsbar).
You may also want to adjust the masking threshold, as noted below. You can
do this easily by just adding a line to spm_defaults.m with the desired
threshold. (For example: defaults.mask.thresh = 0.3;) We have found that
0.8 is too high for data collected on the Berkeley scanner. An empirical
test of voxels eliminated inside & outside the brain by differing threshold
levels validated 0.3 as a better threshold for data collected here, at
least for one set of acquisition parameters.
Cheers,
Charlotte
At 08:36 PM 2/5/2006, you wrote:
>Hi Martin,
>
>I suspect this happening because SPM sets the threshold for analysis
>to be at 80% of the global mean.
>
>In spm_fmri_spm_ui.m line(410)
>try
> TH = g.*gSF*defaults.mask.thresh;
>catch
> TH = g.*gSF*0.8;
>end
>Unless you apply session specific scaling, gSF = GM./g and GM =100; So
>the threshold is always at 80.
>
>Load SPM.mat for a subject and check what the value of SPM.xM.TH is. I
>suspect this is 80 (unless you apply session specific scaling). Make
>sure this is -inf, save the SPM.mat file and rerun the estimation
>step. The primary reason for the scaling I believe is to keep out
>outliers. When the ROI mask is small, and anatomically defined, such a
>rigid threshold may not be necessary.
>
>Hope that helps.
>
>Satra
>
>--
>Satrajit Ghosh, PhD
>
>Speech Communications Group
>Research Lab of Electronics, MIT
>
>
>On 2/5/06, Martin Zalesak <[log in to unmask]> wrote:
> > Dear all,
> >
> > I am sorry to be sending this again, but I really want to find out
> > the answer to this problem. I think this could be addressed by
> > someone who has detailed knowledge of the SPM2 machinery.
> >
> > I am trying to run the SPM GLM on native space BOLD images as
> > follows: I created an anatomical ROI on native space anatomical image
> > first. Then I applied this ROI as a mask to all my BOLD images, thus
> > creating partial brain BOLD volumes in native (i.e. non-normalized) space.
> >
> > Now I want to run the GLM on these partial brain images to obtain the
> > beta parameter estimates. When I check the results, I see that the
> > resultant analysis mask (mask.img) looks very much like the
> > anatomical mask that I used in the first place, which is good.
> > However, when I look at the beta images, I notice that most of the
> > voxels within the mask (defined by mask.img) have NaN values. I
> > thought that all voxels within the space defined by the mask should
> > have non-zero beta values.
> >
> > That's a problem as I need to get a beta value for every voxel that
> > is inside the mask. Does anyone have any ideas or suggestions? How do
> > I fill the whole ROI with beta values? Does this have anything to do
> > with the fact that I am not using smoothing and normalization?
> >
> > Please advise. Thank you,
> > Martin
> >
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