Dear Jon,
The simplest (and easiest to sort out) problem is that you have not reset
your origin on the self- made mask. Analyze will write out this image with
no associated mat file and spm99 will chose the central voxel as the orign.
As this will not match up with you functional data (whose origin will be at
the ac point if you apatially normalized your activation scans), your blobs
will not fall inside your mask and you will get zilch. Use the reorientate
image function in spm99. Display the average brain you used to create the
mask, note down it's origin. Display your mask image and move it in the x, y
and z plane until it has the same origin point; press reorientate image and
the mask will be saved with a mat file. It should then work for your svc.
Cheers.
Alex.
-----Original Message-----
From: Jon Brooks
To: [log in to unmask]
Sent: 6/22/01 3:01 PM
Subject: problems using a brain mask
Dear All,
In response to reviewers comments on a paper
we just submitted, I have been asked to reanalyse
some fMRI data using a small volume correction.
Rather than pick spheres or define cubes I want
to use a mask determined from our average brain
(made from the anatomicals for each subject in the
study). So using Analyze I have created a mask by
using "image edit" to block out the relevant regions.
The selected regions are set to 255 and everything else
to 0. I then smoothed the mask in SPM99 using a 3mm FWHM
kernel. Because I want to see the effect of the masking on
the resultant SPMs I followed a suggestion in an earlier
thread and applied the mask to the first time point
of the fMRI data. This should restrict the analysis to
a volume corresponding to the mask.
Using a standard fMRI design matrix I ran the appropriate
analysis and went to look at the results. I got zilch!
With the unrestricted analysis and a corrected p(0.05) I
got lots of blobs from a sample volume of 630 resels, in
my restricted analysis only 0.1 resels are included in
the analysis. I'm really out of my depth here as to the
reason why this analysis is failing so spectacularly,
can anyone suggest what's going wrong?
Any instructions or suggestions would be greatly appreciated.
Cheers,
Jon.
_____________________________________________________
Jonathan Brooks Ph.D. (Research Fellow)
Magnetic Resonance and Image Analysis Research Centre
University of Liverpool, Pembroke Place, L69 3BX, UK
tel: +44 151 794 5629 fax: +44 151 794 5635
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