Differences

This shows you the differences between two versions of the page.

--- biac:analysis:roi_et [2011/04/25 18:47]
petty
+++ biac:analysis:roi_et [2023/02/23 18:43] (current)
@@ Line 1: / Line 1: @@
 ====== Region of Interest Based Eyetracking Analysis ======
-These steps were created to gather eyetracking information based on specific regions of interest drawn on stimuli from the experimental task.  The following assumes your task was image based, ( or images can be created to mimic the task ), there is XML behavioral output from the task, and your eyetracking was collected through Cigal or Viewpoint.
+These steps were created to gather eyetracking information based on specific regions of interest drawn on stimuli from the experimental task.  The following assumes your task was image based, ( or images can be created to mimic the task ), there is XML behavioral output from the task, and your eyetracking was collected through Cigal or Viewpoint.  The steps are run based (excluding drawing the ROIs).
 ===== Behavioral XML =====
@@ Line 127: / Line 127: @@
 ===== Merge Behavioral XML and ROI XML Data =====
-Now its necesary to merge the two sets of XML data together using **"bxh_eventmerge"**.  This will insert your ROI data into the associated nodes from your behavioral XML.
+Now its necesary to merge the two sets of XML data together using **"bxh_eventmerge"**.  This will insert your ROI data into the associated nodes from your behavioral XML.  This must be run on a machine with the xcede tools.  The inputs are the behavioral XML and the ROI XML from the previous step.
 <file sh merge_rois_into_behav.sh>
@@ Line 139: / Line 139: @@
   BEHAVIORAL_run.xml \
   my_drawn_ET_ROI.xml
+##  comments
+# grabexcludeset ignores any matches
+# mergeeventpath is the path to the XML nodes from the ROI.xml, the example above represents
+#  <rois>
+#       <roi/>
+#  </rois>
+# 'value[@name="imgName"]' means that i am matching on name="imgName" in both behav and ET_ROI files (INPUTQUERY)
+# my GRABQUERY is just '.', means grab everything from ET_ROI.xml matches
 </file>
@@ Line 176: / Line 186: @@
+===== Preprocess Eyetracking Data =====
+This will convert either Cigal or Viewpoint wks files into CSV ( comma-separated values ), with distinct headers for each column.  If the data is in WKS normalized space, it needs to be converted into screen resolution using the same values used in the ROI drawing step.  Also, if WKS data is not time-locked to the zero point of your task, a marker should be sent from your task to the eyetracking recording to mark the zero time.
+Cigal files will already be in pixel resolution.  Jim has also provided some tools to calibrate in cigal, then apply to the viewpoint software.  If [[jvs:cigal:eyetracking:eyecalwks|these]] methods have been used, the output will also be in pixel resolution.  Otherwise, the valid resolution must be input into the preprocessing step.
+Chris Petty has written a perl script (**preprocess_eyetracking.pl**) to handle the preprocessing with various input flags.  Can be copied from \\Munin\Data\Programs\User_Scripts\petty, or run directly from cluster nodes.
+<code perl>
+USAGE: preprocess_eyetracking.pl [options] --input FILE --output FILENAME --type TYPE
+where [OPTIONS] may be the following:
+   --debug        enables debug mode
+   --help         displays this help
+   --input        eyetracking input data *
+   --output       name of output file *
+   --type         type of eyetracking data (raw,cigal) *
+   --onsetMarker  character than marks zero point in raw files
+   --convertpix   flag to convert to pixel dimensions
+   --xres         x_screen resolution (only needed if not in pixels)
+   --yres         y_screen resolution (only needed if not in pixels)
+</code>
+<code>perl preprocess_eyetracking.pl --input subj_12345.wks --output subj_12345.preproc.wks --type raw --onsetMarker M --convertpix --xres 1024 --yres 768 </code>
+  *--input: is your eyetracking data ( either .wks or cigal eyepos file )
+  * --output: is the name to output your csv file  ( .txt, .csv, .wks are all file )
+  * --type: represents "cigal" or "raw" ( different things happen depending on the type, "raw" represents viewpoint files )
+if **wks** input, --onsetMarker is required if the data is not time-locked to your zero point.  The time where --onsetMarker is found within the eyetracking data will be subtracted from all following input times, therefore zeroing the onsets.
+if **wks** input is not in pixel dimensions as mentioned above, --convertpix with tell the script to convert the normalized space into pixel dimensions using the X and Y values ( --xres, --yres )
+This output will be used in all future steps.
+For example:
+<file csv>
+VP_Code,TotalTime,DeltaTime,X_Gaze,Y_Gaze,Region,PupilWidth,PupilAspect
+,0,M
+,0.000900000000001455,0.033671,391,231,0,0.0844,1.0000
+,0.034000000000006,0.033072,391,231,0,0.0813,0.9630
+,0.0674000000000063,0.033401,391,231,0,0.0781,0.9615
+,0.100700000000003,0.03333,391,231,0,0.0844,0.9630
+,0.134100000000004,0.033404,391,231,0,0.0781,0.9615
+,0.167400000000001,0.033327,403,229,0,0.0781,0.9615
+,0.200800000000001,0.033382,414,228,0,0.0813,1.0000
+,0.234200000000001,0.033359,414,228,0,0.0813,1.0000
+,0.267600000000002,0.033438,426,227,0,0.0813,1.0000
+,0.300899999999999,0.033295,437,226,0,0.0781,0.9615
+,0.334299999999999,0.033418,449,225,0,0.0781,0.9615
+,0.36760000000001,0.03331,449,225,0,0.0813,1.0000
+,0.40100000000001,0.033379,460,224,0,0.0781,0.9615
+,0.434400000000011,0.03336,472,209,0,0.0781,1.0000
+,0.467800000000011,0.033405,460,224,0,0.0781,0.9615
+</file>
+===== Calculate Eyetracking Hits =====
+Hits are considered eyetracking points where gaze was within ROIs defined in step 1, during the duration of each image.
+Chris has written a perl script (**merge_eyetracking.pl**), which takes the merged behavioral-ROI xml and the preprocessed eyetracking data from the last step to calculate the hits.
+The script can be copied from: \\Munin\Data\Programs\User_Scripts\petty, or run directly from cluster nodes.
+<code>
+USAGE: merge_eyetracking.pl [options] --eyetracking FILE --behavioral XML --output XML --type
+where [OPTIONS] may be the following:
+   --debug #        enables debug mode
+   --help         displays this help
+   --eyetracking  eyetracking input data *
+   --behavioral   behavioral XML input *
+   --output       name of output XML *
+   --type         type of eyetracking data (raw,cigal) *
+</code>
+  * --eyetracking: preprocessed eyetracking CSV file
+  * --behavioral : behavioral XML ( with ROIs merged )
+  * --ouput      : name of .XML to output file
+  * --type       : cigal or raw ( same type from preprocessing step )
+<code>perl merge_eyetracking.pl --eyetracking subj_12345_run1.preproc.wks --behavioral merged-subj12345_run1.xml --output subj1234_run1_roiHit.xml --type raw</code>
+The processing script will add elements to the behavioral XML that represent hits and samples of valid eyetracking points from within your duration, this instance has 120 valid sample, with more than 50% inside the ROI:
+<HTML>
+  <event type="image" units="sec">
+    <onset>34.5</onset>
+    <duration>4</duration>
+    <value name="imgName">37M_CA_C.bmp</value>
+    <value name="regType">positive</value>
+    <value name="trialType">FACE</value>
+    <value name="response">1</value>
+    <value name="RT">1026</value>
+    <roi type="circle">
+      <name>face</name>
+      <center>515 443</center>
+      <size>446 474</size>
+      <units>pixels</units>
+      <value name="hits">62</value>
+      <value name="hit_percent">51.67</value>
+    </roi>
+    <value name="samples">120</value>
+  </event>
+ </HTML>
+At this point you could use these additional XML elements when extracting your onsets for FSL, etc by including some hit criteria in your xcede_extract_schedules.pl queries.
+===== Visualizing Eyetracking Points in Matlab =====
+Once eyetracking has been preprocessed, behavioral/ROI XML files have been created, you can visualize the points in matlab.  The following script will run a function that will re-draw the screen and image, redraw the ROI if thats the function chosen and plot the eyetracking points.  If ROIs are included, hits and misses will be differentiated.
+Functions can be added to matlab path: \\Munin\Data\Programs\User_Scripts\petty\matlab\ or copied into a local location.
+To run the plotter:
+<file matlab et_visualization_sample.m>
+%% add biac tools if needed
+%run /usr/local/packages/MATLAB/BIAC/startup.m
+%%add my functions
+%addpath \\Munin\Data\Programs\User_Scripts\petty\matlab\
+addpath /home/petty/net/munin/data/Programs/User_Scripts/petty/matlab/
+%%XML with behavioral and ROIS
+XML_docname = '11436_run04_roiHits_pupil.xml';
+%%preprocessed eyetracking data
+ET_filename = '11436_run4_pre.txt';
+%%Path to your actual images, an array if multiple locations possible
+imgPath = {'//hill/data/Dichter/AutReg.01/Stimuli/AutReg.01/','//hill/data/Dichter/AutReg.01/Notes/SubjectPics/PS06'};
+%%Image attribute name from behavioral XML [value=name"THIS"]
+imgAttr = 'imgName';
+%%screen resolution of stimulus computer
+xRes = 1024;
+yRes = 768;
+scrSize = [ xRes yRes ];
+%%turn on scanpath lines
+linesOn = 1;
+%%turn on pause
+withPause = 0; %1=on, this pauses between every point
+%%run the function
+%%this will show image, ROI, and ET points
+ROI_redraw(XML_docname,ET_filename,imgPath,imgAttr,scrSize,linesOn,withPause);
+%%this will only show image and ET points
+%ET_plot(XML_docname,ET_filename,imgPath,imgAttr,scrSize,linesOn,withPause);
+</file>
+The output will look like this:
+{{:biac:analysis:plotter_example.png?800|}}
+Hits are green circles inside the ROI, misses are red Xs outside.  Since **linesOn** was turned on, there is a yellow gaze path from one point to the next.  If **withPause** was turned on, there would be a slight pause between each point.
+Currently, to move to the next image in the XML, just close the current figure.  If you want to stop the redrawing, "ctrl + c" inside matlab to kill the loop.  There are some updates planned to the controls.
+Also, if you just have the behavioral XML and preprocessed ET data, you can run the function **ET_plot** instead.  This will look at all images and ignore any ROIs, otherwise and ROI must be present for the image to get plotted.
+===== PupilOmetry in Matlab =====
+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

Brain Imaging & Analysis Center

User Tools

Site Tools

Differences

Page Tools