Dear Silvia,
If I understand correctly, your reviewer is asking you 2 things:
1) "Results should also be presented in terms of z-score (T-score) averaged
on unthresholded contrast image for regions of interest that are typically
involved in the disease [...]"
There are certainly good ways to do this inside SPM, but a very simple and
intuitive program that allows you to to this is Chris Rorden's MRIcro.
Just open your con* images using MRIcro, draw ROIs on the regions "typically
involved in the disease", than use the button "ROI min, mean and max" to
extract these information, as well the number of voxels in the ROI, the
number of non-zero and positive voxels, and the standard deviation.
Right-clicking the same button saves a list of the voxels' coordinates and
their values in a tabulated TXT file, which you can export to a spreadsheet
and use for additional calculations.
Note that you can save the ROI in a separate file, so that you can use it
for other images, without drawing them again.
2) "[...] Furthermore the z-scores image should be also presented
unthresholded (to create them, again disallow statistical threshold in SPM)"
You may use the "Display" function of SPM to open the con* images. If you
don't like the grayscale image, change the colormap. To use the colorful
"Jet" colormap, for example, type
>> colormap('jet')
at the Matlab prompt while the image is shown in the SPM Graphics Window. If
you have your own RGB colormap, use
>> colormap(yourmaphere)
Regardless if you change the colormap or not, remember to put a colorbar
next to your images, so that the readers of your paper can have an idea of
how high are your scores, and how the colors are mapped.
Hope it helps. Good luck!
Anderson
PS: I've just seen Matthew's post. Yes, there are many ways to do this!
On Wed, 23 May 2007 16:09:57 +0200, silviamorbelli
<[log in to unmask]> wrote:
>Dear Anderson,
>Thanks a lot for your precious answer. I found the con*.img and hdr in the
working directory of my SPM statistics. Moreover I read carefully the paper
from Jernigan et al. which is very informative indeed and that I already had
noticed. However, what I was unable to undesrtand is how to obtain (or to
find out) the correspondent Z-scores values for the voxels/clusters of
these con*.img maps.
>Please, could you help me again?
>Really many, many thanks...
>best
>Silvia
>For your convenience, I enclose you here the request of the referee :
>"Results should also be presented in terms of z-score (T-score) averaged on
unthresholded contrast image for regions of interest that are typically
involved in the disease (disallow F and T thresholds in SPM for this).
Furthermore the z-scores image should be also presented unthresholded (to
create them, again disallow statistical threshold in SPM)".
>
>
>
>
>---------- Initial Header -----------
>
>From : "SPM (Statistical Parametric Mapping)" [log in to unmask]
>To : [log in to unmask]
>Cc :
>Date : Thu, 17 May 2007 16:40:19 +0100
>Subject : Re: [SPM] unthresholded maps
>
>
>
>
>
>
>
>> Dear Silvia,
>>
>> Just open the contrast images generated by SPM, i. e. the files named
>> con*.hdr+img. They should be the unthresholded maps that your reviewer is
>> asking to see.
>> A very good paper on the advantages of unthresholded maps is Jernigan et al
>> (2003), Hum Brain Mapp 19:90-95. Have a look at it.
>>
>> Anderson
>>
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