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--- biac:analysis:roi_et [2011/04/25 20:23]
petty
+++ biac:analysis:roi_et [2023/02/23 18:43] (current)
@@ Line 355: / Line 355: @@
 ===== PupilOmetry in Matlab =====
-{{:biac:analysis:2006_urry_neuro.pdf|Urry et al}}
+A matlab script based on pupilometry steps from {{:biac:analysis:2006_urry_neuro.pdf|Urry et al}} can be run to denoise pupil dilation data found in the preprocessed viewpoint WKS or cigal eyetracking files.
+The result will be a pupilchange element added to your behavioral+ROI XML.
+This example node has all previous steps run, pupil was smaller then the .5sec before image by 2.9% :
+<HTML>
+   <event type="image" units="sec">
+      <onset>17.141</onset>
+      <duration>4</duration>
+      <value name="imgName">HAI_21.bmp</value>
+      <value name="regType">look</value>
+      <value name="trialType">HAI</value>
+      <value name="response">2</value>
+      <value name="RT">1212</value>
+      <roi type="block">
+         <name>object</name>
+         <origin>260 258</origin>
+         <size>500 205</size>
+         <units>pixels</units>
+         <value name="hits">10</value>
+         <value name="hit_percent">8.47</value>
+      </roi>
+      <value name="samples">118</value>
+      <value name="pupilChange">-0.029751</value>
+   </event>
+</HTML>
+The pupilOmetry function can be found: \\Munin\Data\Programs\Users_Scripts\petty\matlab\ or just added to your path.
+This example script will run pupilOmetry on preprocessed eyetracking data and create the new XML with the added element:
+<file matlab run_pupilOmetry_sample.m>
+%% add BIAC tools if needed
+%run /usr/local/packages/MATLAB/BIAC/startup.m
+%% add path to pupilOmetry function
+%addpath /home/petty/net/munin/data/Programs/User_Scripts/petty/matlab/
+%addpath \\Munin\Data\Programs\User_Scripts\petty\matlab\
+%%input XML ( merged behavioral + ROI )
+xmlName = '/home/petty/eyetracking/autreg/11436_run04_roiHits.xml';
+%%preprocessed eyetracking output
+ET_filename = '/home/petty/net/hill/data/Dichter/AutReg.01/Data/Eyetracking/subj1234_run1_pre.wks';
+%%the attribute to match images with from the inputXML
+imgAttr = 'imgName';
+%%output name of the XML with added pupilOmetry data. will be everything from input + pupilchange
+outName = '/home/petty/eyetracking/autreg/11436_cigal_pupil2.xml';
+%%show the denoising plots
+plot = 0; %1 to show, 0 to skip
+%%run the actual function
+pupilOmetry(xmlName,ET_filename,imgAttr,outName,plot);
+</file>
+===== future =====
+  * If there are any suggestions for added features, or something just isn't right please contact Chris

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