notes.txt

NiiStat includes some "global" values. These are for advanced uses. Be aware that a global value stay in effect until you quit matlab or you set it to empty. Therefore, once you set a global, all future calls to nii_stat will use this value.

global global_flContrast
global_flContrast = [1 -1]; %this will be zero padded, so if you have four conditions (plus implicit intercept) it will be [1 -1 0 0 0]
nii_stat
...
global_flContrast = []; %remove this so future calls treat each column as nuisance regressor

The value "global_roiMask" allows you to explicitly restrict regions of interest.

global global_roiMask
global_roiMask = [1 3 4];
nii_stat

l = load('LM1045.mat')
labels = cellstr(l.dti_jhu.label)
'1|SFG_L|superior frontal gyrus (posterior segment) left|1'
'3|SFG_PFC_L|superior frontal gyrus (prefrontal cortex) left|1'
'4|SFG_PFC_R|superior frontal gyrus (prefrontal cortex) right|1'


indx = roiMask;
labels = labels(indx,:);
labels
class(labels)
index = strfind(cellstr(labels),'|1');
index = ~cellfun('isempty',index);
smalllabels = labels(index,:);
class(smalllabels)


 indx = [1 3 126 185 ]
 labels3 = labels(indx,:);
index = strfind(cellstr(labels3),'|1');
size(les_names,1)
B = triu(ones(size(A)),1);

B = sum(sum(triu(ones(size(les_names,1)),1)))

(sum(sum(triu(ones(size(les_names,1)),1))) == numel( les(1, :))  || ;

  numel(les(1, :))
    B = sum(sum(triu(ones(size(les_names,1)),1)))

   nRow = size(les_names,1))
   nRow = 110
   sum(sum(triu(ones(nRow),1)))

   sum(sum(triu(ones(nRow,1)))
    triu(zeros(110))

    if (size(les_names,1) > 1) &&  (size(les_names,1) == numel( les(1, :)))   %for ROI analyses
  %this next bit allow us to remove ROIs
  % global roiMask
  % roiMask = [1 3 4]; %only include these regions of interest
  global roiMask
  if ~isempty(roiMask)
    if min(roiMask(:)) < 1 || max(roiMask(:)) > size( les(1, :),2)
        error('global roiMask must have values in the range 1..%d', size( les(1, :),2));
    end
    global roiMaskDeleteItems;
    if ~isempty(roiMaskDeleteItems) && roiMaskDeleteItems
        rMask = roiMask; %delete items in ROI mask, [1 2 5] removes 1st, 2nd, 5th col
    else
        rMask = 1: size(les_names,1); rMask(roiMask)=[]; %[1 2 5] preserves 1st, 2nd 5th
    end
    les(:, rMask)=[]; %remove columns
    les_names(rMask,:) = [];
  end
end