Merge branch 'master' of https://github.com/canlab/CanlabCore

CanlabCore/@atlas/select_atlas_subset.m

@@ -20,6 +20,9 @@
 % 'labels_2' : If you enter any field name in the object, e.g., labels_2,
 % the function will search for keyword matches here instead of in obj.labels.
 %
+% 'exact' : If you enter 'exact', function will not look for overlaps in
+% names, and only look for exact string matches.
+%
 % Examples:
 % 
 % atlasfile = which('Morel_thalamus_atlas_object.mat');
@@ -59,6 +62,9 @@
 % Edited by tor, 12/2019, to use any field to select labels; and update
 % auxiliary label fields too.
 %
+% Edited by Michael Sun, 09/04/2023, added an 'exact' flag, so that users
+% can select to match string labels exactly and not capture regions with
+% overlapping labels e.g., Cblm_Vermis_VI and Cblm_Vermis_VII.
 
 % -------------------------------------------------------------------------
 % DEFAULTS AND INPUTS
@@ -67,6 +73,7 @@
 strings_to_find = [];
 integers_to_find = [];
 doflatten = false;
+doexact=false;
 
 % for entry of optional field to search for keywords
 myfields = fieldnames(obj);
@@ -87,6 +94,7 @@
              case 'flatten', doflatten = true;
 
                  %             case 'xxx', xxx = varargin{i+1}; varargin{i+1} = [];
+            case 'exact', doexact = true;
 
             otherwise
 
@@ -117,14 +125,22 @@
 for i = 1:length(strings_to_find)
 
     % Find which names match
-    wh = ~cellfun(@isempty, strfind(obj.(mylabelsfield), strings_to_find{i}));
-    if strmatch(mylabelsfield, 'label_descriptions')
-        wh=wh';
+    if doexact == false
+        wh = ~cellfun(@isempty, strfind(obj.(mylabelsfield), strings_to_find{i}));
+        if strmatch(mylabelsfield, 'label_descriptions')
+            wh=wh'; 
+        end
+
+        to_extract = to_extract | wh;
+    % Addition by Michael Sun 09/04/2023: Match strings exactly
+    else
+        wh = strcmp(obj.(mylabelsfield), strings_to_find{i});
+        if strmatch(mylabelsfield, 'label_descriptions')
+            wh=wh'; 
+        end
+
+        to_extract = to_extract | wh;
     end
-
-
-    to_extract = to_extract | wh;
-
 end
 
 % -------------------------------------------------------------------------

CanlabCore/Data_processing_tools/downsample_scnlab.m

@@ -15,6 +15,17 @@
 %   **new_samprate:**
 %        desired sampling rate in Hz
 %
+%   **doplot:**
+%        visualize the plot. Default: off
+% 
+%   **method:**
+%        Interpolation method. Default: linear
+%        'linear' (default) | 'nearest' | 'next' | 'previous' | 'pchip' | 
+%        'cubic' | 'v5cubic' | 'makima' | 'spline'
+% 
+%   **extrap:**
+%        Extrapolation strategy, specified as 'extrap' or a real scalar value.
+% 
 % ..
 %    I prefer this to matlab's downsample.m because linear interpolation is
 %    robust and does fewer weird things to the data.
@@ -30,10 +41,30 @@
 %    % every 100 / TR = 100/.5 = 200 samples
 %
 %    [yi, xi] = downsample_scnlab(y, 100, .5)
+%    [yi, xi] = downsample_scnlab(y, 100, .5, 'doplot', 'method', 'spline')
 %
+% Programmers notes:
+% 8/25/2023 - Byeol
+% Add more method options for interp1 function.
+
 
 doplot = 0;
-if length(varargin) > 0, doplot = varargin{1}; end
+method = 'linear';
+extrapolation = 'extrap';
+
+for i = 1:length(varargin)
+    if ischar(varargin{i})
+        switch varargin{i}
+            % functional commands
+            case {'doplot'}
+                doplot = 1;
+            case {'method'}
+                method = varargin{i+1};
+            case {'extrap'}
+                extrapolation = varargin{i+1};
+        end
+    end
+end
 
 downsamplerate = orig_samprate ./ new_samprate;
 
@@ -49,7 +80,7 @@
 xi = linspace(0, nobs, nobs_out);
 
 
-yi = interp1(x, y, xi, 'linear', 'extrap');
+yi = interp1(x, y, xi, method, extrapolation);
 
 if doplot
 

CanlabCore/Visualization_functions/canlab_results_fmridisplay.m

@@ -56,11 +56,8 @@
 %        'compact2'        A single row showing midline saggital and axial slices
 %        'multirow'        A series of 'compact2' displays in one figure for comparing different images/maps side by side
 %        'regioncenters'   A series of separate axes, each focused on one region
-%
-%        'full' for full montages of axial and sagg slices.
-%
-%        'full hcp' for full montage, but with surfaces and volumes from
-%        HCP data
+%        'full2' for a slightly less full montage that avoids colorbar overlap issues
+%        'full hcp' for full montage, but with surfaces and volumes from HCP data
 %
 %        'compact' [default] for single-figure parasagittal and axials slices.
 %
@@ -161,7 +158,8 @@
 if ischar(input_activation)
 
     if strcmp(input_activation, 'compact') || strcmp(input_activation, 'compact2') || strcmp(input_activation, 'full') ...
-            || strcmp(input_activation, 'multirow') || strcmp(input_activation, 'coronal') || strcmp(input_activation, 'sagittal')
+            || strcmp(input_activation, 'multirow') || strcmp(input_activation, 'coronal') || strcmp(input_activation, 'sagittal') ...
+            || strcmp(input_activation, 'full2') || strcmp(input_activation, 'full hcp') 
 
         % Entered no data map; intention is not to plot blobs, just create underlay
         varargin{end + 1} = 'noblobs'; 
@@ -247,6 +245,9 @@
 wh = strcmp(varargin, 'full hcp');
 if any(wh), montagetype = varargin{find(wh)}; varargin(wh) = []; end
 
+wh = strcmp(varargin, 'full2');
+if any(wh), montagetype = varargin{find(wh)}; varargin(wh) = []; end
+
 wh = strcmp(varargin, 'compact');
 if any(wh), montagetype = varargin{find(wh)}; varargin(wh) = []; end
 
@@ -477,6 +478,36 @@
             wh_montages = [1 2 3 4];
             wh_surfaces = [1 2 3 4];
 
+        case 'full2'
+
+            % saggital
+            [o2, dat] = montage(o2, 'saggital', 'wh_slice', xyz, 'onerow', 'noverbose');
+            shift_axes(-0.02, -0.04);
+
+            % coronal
+            axh = axes('Position', [-0.02 0.37 .1 .17]);
+            o2 = montage(o2, 'volume_data', dat, 'coronal', 'slice_range', [-40 50], 'onerow', 'spacing', 8, 'noverbose', 'existing_axes', axh);
+
+            % axial
+            axh = axes('Position', [-0.02 0.19 .1 .17]);
+            o2 = montage(o2, 'volume_data', dat, 'axial', 'slice_range', [-40 50], 'onerow', 'spacing', 8, 'noverbose', 'existing_axes', axh);
+
+            allaxh = findobj(gcf, 'Type', 'axes');
+            disp(length(allaxh));
+            for i = 1:(length(allaxh)-36)
+                pos1 = get(allaxh(i), 'Position');
+                pos1(1) = pos1(1) - 0.03;
+                set(allaxh(i), 'Position', pos1);
+            end
+
+            % surface
+            o2 = surface(o2, 'axes', [0.1 0.74 .25 .25], 'direction', 'hires left', 'orientation', 'medial');
+            o2 = surface(o2, 'axes', [0.3 0.74 .25 .25], 'direction', 'hires right', 'orientation', 'medial');          
+            o2 = surface(o2, 'axes', [0.5 0.74 .25 .25], 'direction', 'hires left', 'orientation', 'lateral');
+            o2 = surface(o2, 'axes', [0.7 0.74 .25 .25], 'direction', 'hires right', 'orientation', 'lateral');
+
+            wh_montages = [1 2 3 4];
+            wh_surfaces = [1 2 3 4];
 
         case 'compact2'  % creates a new figure
             %subplot(2, 1, 1);