running analyses

silverlab · Feb 11, 2013 · c1934cc · c1934cc
1 parent 4423f99
commit c1934cc
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Showing 7 changed files with 35 additions and 30 deletions.
diff --git a/users/Rachel/LGN_Code/rd_centerOfMassGroupAnalysis.m b/users/Rachel/LGN_Code/rd_centerOfMassGroupAnalysis.m
@@ -49,7 +49,7 @@
 end
 
 % subjects = 1:size(subjectDirs,1);
-subjects = 7:8;
+subjects = [1 2 3 4 5 8];
 nSubjects = numel(subjects);
 
 mmMat = repmat(voxelSize,nSubjects,1);

diff --git a/users/Rachel/LGN_Code/rd_centerOfMassNormGroupAnalysis.m b/users/Rachel/LGN_Code/rd_centerOfMassNormGroupAnalysis.m
@@ -4,13 +4,13 @@
 [subjectDirs3T subjectDirs7T] = rd_lgnSubjects;
 
 scanner = '7T';
-mapName = 'betaM';
+mapName = 'betaM-P';
 prop = 0.2;
 analysisExtension = sprintf('centerOfMassNorm_%s_prop%d_*', mapName, round(prop*100));
 hemis = [1 2];
 
 plotFigs = 1;
-saveFigs = 1;
+saveFigs = 0;
 saveAnalysis = 0;
 
 MCol = [220 20 60]./255; % red
@@ -48,7 +48,7 @@
 cVarThresh = 0;
 
 % subjects = 1:size(subjectDirs,1);
-subjects = [7 8];
+subjects = [1:4];
 nSubjects = numel(subjects);
 
 %% File I/O

diff --git a/users/Rachel/LGN_Code/rd_getAnalysisFilePath.m b/users/Rachel/LGN_Code/rd_getAnalysisFilePath.m
@@ -3,7 +3,8 @@
 % function filePath = rd_getAnalysisFilePath(subjectDirs, scanner, subject, hemi, analysisExtension)
 %
 % gets the filepath to a specific analysis file for any subject and
-% hemisphere.
+% hemisphere. if no analysis file is specified, will still return the file
+% directory.
 
 allowWildcardExtension = 1;
 
@@ -44,5 +45,4 @@
 else
     fileName = [];
     filePath = [];
-    fprintf('\nSorry, the analysis file was not sufficiently specified. Check arguments.\n\n')
 end
diff --git a/users/Rachel/LGN_Code/rd_lgnSubjects.m b/users/Rachel/LGN_Code/rd_lgnSubjects.m
@@ -12,12 +12,10 @@
 
 subjectDirs7T = {'KS_20111212_Session', 'KS_20111212_15mm', 'ROIX01';
                 'AV_20111213_Session', 'AV_20111213', 'ROIX01';
-                'KS_20111214_Session', 'KS_20111214', 'ROIX01/Runs1.3-7';
+                'KS_20111214_Session', 'KS_20111214', 'ROIX01/Runs1-7';
                 'RD_20111214_Session', 'RD_20111214', 'ROIX01';
                 'KS_20111212_Session', 'KS_20111212_125mm', 'ROIX01';
-                'MN_20120806_Session', 'MN_20120806', 'ROIX01';
+                'MN_20120806_Session', 'MN_20120806', 'Runs1-5/ROIX02';
                 'SB_20120807_Session', 'SB_20120807', 'ROIX01';
                 'JN_20120808_Session', 'JN_20120808', 'ROIX01';
-                'RD_20120809_Session', 'RD_20120809_axial', 'ROIX01';
-%                 'JN_20120808_Session', 'JN_20120808_spmDC', 'ROIX01';
-                'JN_20120808_Session', 'JN_20120808_fslDC', 'ROIX01'};
+                'RD_20120809_Session', 'RD_20120809_axial', 'ROIX01'};
diff --git a/users/Rachel/LGN_Code/rd_mrXformCentersCoordsToVolCoords.m b/users/Rachel/LGN_Code/rd_mrXformCentersCoordsToVolCoords.m
@@ -1,4 +1,4 @@
-% rd_mrXformCentersCoordsToVolCoords.m
+function rd_mrXformCentersCoordsToVolCoords(hemi, mapName)
 %
 % Transforms center of mass cordinates from epi coords to volume coords, in
 % order to reorient them to a canonical upright orientation.
@@ -10,9 +10,9 @@
 % 2013 Feb 6
 
 %% Setup
-hemi = 1;
-
-mapName = 'betaM-P';
+% hemi = 1;
+% 
+% mapName = 'betaM-P';
 
 switch mapName
     case 'betaM-P'

diff --git a/users/Rachel/LGN_Code/rd_normalizeCenterOfMass.m b/users/Rachel/LGN_Code/rd_normalizeCenterOfMass.m
@@ -19,12 +19,12 @@ function rd_normalizeCenterOfMass(hemi, mapName)
     case 'betaP'
         prop = 0.8;
     otherwise
-        error ('mapName not recognized when setting prop and betaCoefs')
+        error ('mapName not recognized when setting prop')
 end
 
 plotFigs = 1;
-saveAnalysis = 0;
-saveFigs = 0;
+saveAnalysis = 1;
+saveFigs = 1;
 
 %% colors
 MCol = [220 20 60]./255; % red
@@ -85,14 +85,15 @@ function rd_normalizeCenterOfMass(hemi, mapName)
         ipVoxSize = mrSESSION.inplanes.voxelSize;
         volVoxSize = [1 1 1];
         xform = mrSESSION.alignment;
-        % find volume ROI coordinates - convert from inplane to volume
+        % Find volume ROI coordinates - convert from Inplane to Volume
         coordsTemp = xformROIcoords(figData.coordsAnatomy, xform, ipVoxSize, ...
             volVoxSize); % coordsAnatomy are in inplane (gems) space
         % For Vol coords, need to switch axi and sag dimensions and need to
-        % flip the A-P and D-V directions
+        % flip the A-P and D-V directions to make it match the epi coords
+        % (and what the plots expect)
         coords(1,:) = coordsTemp(3,:); % Sag --> x
-        coords(2,:) = coordsTemp(2,:)*(-1); % Cor --> y, flip A-P
-        coords(3,:) = coordsTemp(1,:)*(-1); % Axi --> z, flip D-V
+        coords(2,:) = coordsTemp(2,:)*(-1); % Cor --> y, flip A-P --> P-A
+        coords(3,:) = coordsTemp(1,:)*(-1); % Axi --> z, flip D-V --> V-D
     otherwise
         error('coordsType not recognized.')
 end
@@ -105,11 +106,12 @@ function rd_normalizeCenterOfMass(hemi, mapName)
     case 'Volume'
         centersTemp{1} = C.centers1Vol;
         centersTemp{2} = C.centers2Vol;
-        % For Vol centers, need to switch axi and sag dimensions
+        % For Vol centers, need to switch axi and sag dimensions and flip
+        % A-P and D-V directions
         for iC = 1:numel(centersTemp)
             centers{iC}(:,1) = centersTemp{iC}(:,3); % Sag --> x
-            centers{iC}(:,2) = centersTemp{iC}(:,2)*(-1); % Cor --> y, flip A-P
-            centers{iC}(:,3) = centersTemp{iC}(:,1)*(-1); % Axi --> z, flip D-V
+            centers{iC}(:,2) = centersTemp{iC}(:,2)*(-1); % Cor --> y, flip A-P --> P-A
+            centers{iC}(:,3) = centersTemp{iC}(:,1)*(-1); % Axi --> z, flip D-V --> V-D
         end
     otherwise
         error('coordsType not recognized.')
@@ -132,7 +134,7 @@ function rd_normalizeCenterOfMass(hemi, mapName)
 
 %% save analysis
 if saveAnalysis
-    save(analysisFile, 'C', 'coords', 'centers', 'centersNorm')
+    save(analysisFile, 'coordsType', 'C', 'coords', 'centers', 'centersNorm')
 end
 
 %% plot figs

diff --git a/users/Rachel/LGN_Code/rd_runIndivAnalysis.m b/users/Rachel/LGN_Code/rd_runIndivAnalysis.m
@@ -10,7 +10,7 @@
         subjectDirs = subjectDirs7T;
 end
 
-subjects = [10 11];
+subjects = [6];
 % subjects = 1:size(subjectDirs,1);
 nSubjects = numel(subjects);
 
@@ -67,9 +67,14 @@
 
 %     % center of mass sequence
 %     rd_centerOfMass_multiVoxData
-%     rd_normalizeCenterOfMass
-%     rd_centerOfMassNormGroupAnalysis (makes the good XZ plots)
-%     rd_centerOfMassGroupAnalysis (used for center of mass interaction)
+    for hemi = 1:2
+        for mapName = {'betaM-P','betaM','betaP'}
+            rd_mrXformCentersCoordsToVolCoords(hemi,mapName{1}); % (if converting to Volume coords)
+            rd_normalizeCenterOfMass(hemi,mapName{1}); % (option for Volume coords)
+        end
+    end
+%     rd_centerOfMassNormGroupAnalysis % (makes the good XZ plots)
+%     rd_centerOfMassGroupAnalysis % (used for center of mass interaction)
 %     rd_centerOfMassGroupMPInteraction
 
 end