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 peak activation and the coordinates
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wang
BIAC Alum

USA
57 Posts

Posted - Feb 08 2005 :  1:18:59 PM  Show Profile  Reply with Quote
Hi,

Does anyone have an easier way to show peak T value of a T-map in a certain region and the corresponding coordinates? The T-map was generated using BIAC scripts with bxh header, not spm format. Many thanks in advance.


Lihong

Edited by - wang on Feb 08 2005 1:30:28 PM

jim.voyvodic
BIAC Faculty

138 Posts

Posted - Feb 08 2005 :  1:59:10 PM  Show Profile  Reply with Quote
Lihong,
I have a command in fScan that will find peak values and their locations. The command in its simplest form is:
fscan inputbxhfile -e adapt
where inputbxhfile is the data set you want to find the maximum
value for. It should be in 16-bit integer format.
By default it will find the peak in the whole volume, but it will also find peaks for multiple ROIs if you have an ROI map, as:
fscan inputbxhfile -e adapt -m roimap
This runs on Golgi (Windows too but it's easier on Golgi).

If you want to try this approach on your data let me know. You may need to add a command or 2 first to make sure your maps are in the appropriate form.

Jim
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charles.michelich
BIAC Alum

USA
183 Posts

Posted - Feb 09 2005 :  10:07:31 AM  Show Profile  Reply with Quote
Lihong,

You can also do this in MATLAB using the max and ind2sub commands. Here is an example using an IRIS ROI:
% Read ROI and tmap
roi = readmr('ROI.bxh');
tmap = readmr('Tmap.bxh');
if ~isequal(size(roi.data), size(tmap.data))
  error('roi and tmap must be the same size');
end

% Find the voxels in the ROI 
roiIndex = 1;  % ROI from the IRIS mseg to process
voxels = find(roi.data == roiIndex);

% Find the max and the location of the max in the ROI
[val,loc] = max(tmap.data(voxels));
[x,y,z] = ind2sub(size(roi.data), voxels(loc));
disp(sprintf('Max of %g found at [%d,%d,%d]', val, x, y, z));
Chuck
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